diff --git a/alphatrion/artifact/artifact.py b/alphatrion/artifact/artifact.py
index bdaa463..edd5db2 100644
--- a/alphatrion/artifact/artifact.py
+++ b/alphatrion/artifact/artifact.py
@@ -56,17 +56,21 @@ def list_versions(self, repo_name: str) -> list[str]:
         return self._backend.list_versions(repo_name)
 
     def pull(
-        self, repo_name: str, version: str, output_dir: str | None = None
+        self, repo_name: str, version_or_filename: str, output_dir: str | None = None
     ) -> list[str]:
         """
         Pull artifacts from the storage.
 
         :param repo_name: the name of the repository to pull from
-        :param version: the version (tag) to pull
+        :param version_or_filename: the version (tag) or filename to pull.
+            For OCI backend, this is always the tag.
+            For S3 backend, if this matches a file name under the repo,
+            that file will be pulled. Otherwise, if this matches a version folder
+            (e.g., "v1"), all files under that folder will be pulled.
         :param output_dir: optional directory to save files to
         :return: list of absolute file paths that were downloaded
         """
-        return self._backend.pull(repo_name, version, output_dir)
+        return self._backend.pull(repo_name, version_or_filename, output_dir)
 
     def delete(self, repo_name: str, versions: str | list[str]):
         """Delete specific versions from a repository."""
diff --git a/alphatrion/artifact/base.py b/alphatrion/artifact/base.py
index 8c82e4a..b8e907f 100644
--- a/alphatrion/artifact/base.py
+++ b/alphatrion/artifact/base.py
@@ -38,7 +38,7 @@ def pull(
         """Pull artifacts from the storage.
 
         :param repo_name: the name of the repository to pull from
-        :param version: the version (tag) to pull
+        :param version: the version (tag) or filename to pull
         :param output_dir: optional directory to save files to
         :return: list of absolute file paths that were downloaded
         """
diff --git a/alphatrion/artifact/s3_backend.py b/alphatrion/artifact/s3_backend.py
index c450929..70e6466 100644
--- a/alphatrion/artifact/s3_backend.py
+++ b/alphatrion/artifact/s3_backend.py
@@ -1,10 +1,3 @@
-"""S3-compatible artifact storage backend (push-only).
-
-This backend supports pushing artifacts to S3 for archival/backup purposes.
-list_versions() and pull() are not implemented - use AWS S3 console, CLI,
-or SDK directly to retrieve artifacts if needed.
-"""
-
 import os
 
 from alphatrion import envs
@@ -166,12 +159,14 @@ def list_versions(self, repo_name: str) -> list[str]:
             raise RuntimeError(f"Failed to list versions: {e}") from e
 
     def pull(
-        self, repo_name: str, version: str, output_dir: str | None = None
+        self, repo_name: str, version_or_filename: str, output_dir: str | None = None
     ) -> list[str]:
         """Pull (download) files from S3.
 
         :param repo_name: Repository path (e.g., "org_id/team_id/exp_id/ckpt")
-        :param version: The filename to download (for flat structure) or folder name (for versioned structure)
+        :param version_or_filename: For S3 backend, if this matches a file name under the repo,
+            that file will be pulled. Otherwise, if this matches a version folder (e.g., "v1"),
+            all files under that folder will be pulled.
         :param output_dir: Optional directory to save files. If None, downloads to current directory.
         :return: List of absolute paths to downloaded files
         """
@@ -182,25 +177,15 @@ def pull(
             download_dir = os.getcwd()
 
         try:
-            # Check if version looks like a filename (has extension) or version folder
-            if "." in version:
-                # Single file: repo_name/version (e.g., "ckpt/checkpoint_123.pt")
-                s3_key = f"{repo_name}/{version}"
-                local_path = os.path.join(download_dir, version)
-
-                self._s3.download_file(self._bucket, s3_key, local_path)
-                return [local_path]
-            else:
-                # Version folder: repo_name/version/* (e.g., "ckpt/v1/*")
-                prefix = f"{repo_name}/{version}/"
+            # First, try as a version folder (e.g., "v1" or "v1.0")
+            prefix = f"{repo_name}/{version_or_filename}/"
 
-                response = self._s3.list_objects_v2(
-                    Bucket=self._bucket, Prefix=prefix, Delimiter="/"
-                )
-
-                if "Contents" not in response:
-                    return []
+            response = self._s3.list_objects_v2(
+                Bucket=self._bucket, Prefix=prefix, Delimiter="/"
+            )
 
+            if "Contents" in response and len(response["Contents"]) > 0:
+                # It's a version folder with files
                 downloaded_files = []
                 for obj in response["Contents"]:
                     s3_key = obj["Key"]
@@ -211,6 +196,24 @@ def pull(
                         downloaded_files.append(local_path)
 
                 return downloaded_files
+
+            # Check if it's an empty folder (no contents) - return empty list
+            # vs a file that doesn't exist (should raise error)
+            # We distinguish by trying to download as a file
+            s3_key = f"{repo_name}/{version_or_filename}"
+            local_path = os.path.join(download_dir, version_or_filename)
+
+            try:
+                self._s3.download_file(self._bucket, s3_key, local_path)
+                return [local_path]
+            except Exception as download_error:
+                error_msg = str(download_error).lower()
+                if "404" in error_msg or "not found" in error_msg:
+                    # Neither folder nor file exists - return empty list
+                    return []
+                raise
+        except RuntimeError:
+            raise
         except Exception as e:
             raise RuntimeError(f"Failed to pull artifacts from S3: {e}") from e
 
diff --git a/alphatrion/experiment/base.py b/alphatrion/experiment/base.py
index 6da6ca0..376bce9 100644
--- a/alphatrion/experiment/base.py
+++ b/alphatrion/experiment/base.py
@@ -1,8 +1,6 @@
 import asyncio
 import contextlib
 import enum
-import os
-import shutil
 import signal
 import uuid
 from abc import ABC, abstractmethod
@@ -11,11 +9,9 @@
 
 from pydantic import BaseModel, Field, model_validator
 
-from alphatrion import envs
 from alphatrion.run.run import Run
 from alphatrion.runtime.contextvars import current_exp_id
 from alphatrion.runtime.runtime import global_runtime
-from alphatrion.snapshot.snapshot import team_path
 from alphatrion.storage import runtime as storage_runtime
 from alphatrion.storage.sql_models import FINISHED_STATUS, Status
 from alphatrion.types import CallableEntry, PostRunHookFn
@@ -212,8 +208,6 @@ async def __aexit__(self, exc_type, exc_val, exc_tb):
             current_exp_id.reset(self._token)
             self._runtime.current_experiment = None
 
-        self._cleanup_files()
-
     def _start(
         self,
         name: str,
@@ -498,14 +492,6 @@ def start(
     ) -> "Experiment":
         raise NotImplementedError
 
-    def _cleanup_files(self):
-        # remove the whole folder once the experiment is done.
-        if (
-            os.path.exists(team_path())
-            and os.getenv(envs.AUTO_CLEANUP, "true").lower() == "true"
-        ):
-            shutil.rmtree(team_path(), ignore_errors=True)
-
     def _start_signal_handlers(self):
         loop = asyncio.get_running_loop()
 
diff --git a/alphatrion/log/load.py b/alphatrion/log/load.py
index 4b64eb6..5a1f270 100644
--- a/alphatrion/log/load.py
+++ b/alphatrion/log/load.py
@@ -35,13 +35,13 @@ async def load_checkpoint(
     output_dir: str | None = None,
 ) -> list[str]:
     """
-    Load checkpoint from artifact registry.
+    Load checkpoint from artifact registry, the path is expected to be in the format of
+    "org_id/team_id/exp_id/ckpt/".
 
     :param id: the id of the experiment.
     :param version: the version of the checkpoint to load, default is "latest".
-        For oci backend, version is the tag of the artifact.
-        For s3 backend, version is the name of the file to load.
-            If version is "latest", the most recently modified file will be loaded.
+        If version is "latest", it will load the latest version (for oci backend) or
+        the file with the latest timestamp (for s3 backend).
     :param type: the type of the checkpoint, can be "experiment" or "agent", default is "experiment".
     :param output_dir: the directory to which the checkpoint will be loaded.
     """
diff --git a/alphatrion/log/log.py b/alphatrion/log/log.py
index c56098e..7507782 100644
--- a/alphatrion/log/log.py
+++ b/alphatrion/log/log.py
@@ -37,7 +37,7 @@ async def log_artifact(
            Takes no arguments and returns nothing. This allows side effects after the artifact is saved,
            such as logging or cleanup.
 
-    :return: the path of the logged artifact.
+    :return: the path of the logged artifact or None if no artifact was logged (e.g., if paths is empty).
         OCI format: {org_id}/{team_id}/{exp_id}/{repo_name}:{version}
         S3 format: {org_id}/{team_id}/{exp_id}/{repo_name}/{version}
     """
diff --git a/alphatrion/server/graphql/resolvers.py b/alphatrion/server/graphql/resolvers.py
index 4e1954c..2f8fe75 100644
--- a/alphatrion/server/graphql/resolvers.py
+++ b/alphatrion/server/graphql/resolvers.py
@@ -951,7 +951,7 @@ async def list_artifact_files(
             arf = runtime.storage_runtime().artifact
             org_id = info.context.org_id
             file_paths = arf.pull(
-                repo_name=f"{org_id}/{team_id}/{repo_name}", version=tag
+                repo_name=f"{org_id}/{team_id}/{repo_name}", version_or_filename=tag
             )
 
             if not file_paths:
@@ -1010,7 +1010,7 @@ async def get_artifact_content(
             # Pull the artifact - ORAS will manage temp directory
             # Returns absolute paths to files in ORAS temp directory
             file_paths = arf.pull(
-                repo_name=f"{org_id}/{team_id}/{repo_name}", version=tag
+                repo_name=f"{org_id}/{team_id}/{repo_name}", version_or_filename=tag
             )
 
             if not file_paths:
diff --git a/alphatrion/snapshot/__init__.py b/alphatrion/snapshot/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/alphatrion/snapshot/snapshot.py b/alphatrion/snapshot/snapshot.py
deleted file mode 100644
index a16cd8d..0000000
--- a/alphatrion/snapshot/snapshot.py
+++ /dev/null
@@ -1,61 +0,0 @@
-from pathlib import Path
-
-from alphatrion.runtime.contextvars import current_exp_id, current_run_id
-from alphatrion.runtime.runtime import global_runtime
-
-"""The snapshot is organized in a hierarchical directory structure as follows:
-└── snapshots
-    ├── team_26c73273-dc1f-40f2-a4ed-7eee35ae05d4
-    │   └── project_7481eedd-86be-4d39-9d0d-679ba83ab7b6
-    │       └── user_95eb9982-56fd-4e1a-8498-28312f4d3ba5
-    │           └── exp_e5b08511-eba4-4ee7-bd10-e632110996b5
-    │               └── run_5b08673b-b2cb-41fb-90f0-c15b450f4433
-    └── team_dcafdce3-dfde-47b4-994c-93880848ca91
-        ├── project_449a560d-cc12-46eb-9058-351cfe56433b
-        │   ├── user_450704dd-37f4-4aa7-97f8-b34e42576b09
-        │   │   ├── exp_c855725d-891f-4f61-8f7d-b6f40c94509f
-        │   │   └── exp_f751ec9c-4aa2-46c5-8cab-1f92af6f001d
-        │   │       ├── checkpoints
-        │   │       ├── run_94a82594-01a7-463f-b63b-ab896be9830e
-        │   │       │   └── result.json
-        │   │       └── run_c0e3c730-c213-4a8e-9e10-7af57fcf8bf9
-        │   └── user_f303c129-c4b5-4f24-957c-d28dd78cce89
-        │       └── exp_efeb5430-6593-4675-969c-325aa25af986
-        │           ├── run_1c89b44d-15de-464a-9e1c-c6aab8a82a7d
-        │           └── run_7990bcf3-f864-4442-ae35-00dd8329f7c5
-        └── project_5cb62b0b-83d3-49fa-956e-cd51df3e7891
-"""
-
-
-def snapshot_path() -> str:
-    runtime = global_runtime()
-    return (
-        Path(runtime.root_path)
-        / "snapshots"
-        / f"team_{runtime.team_id}"
-        / f"user_{runtime.user_id}"
-        / f"exp_{current_exp_id.get()}"
-        / f"run_{current_run_id.get()}"
-    )
-
-
-def checkpoint_path() -> str:
-    runtime = global_runtime()
-    return (
-        Path(runtime.root_path)
-        / "snapshots"
-        / f"org_{runtime.org_id}"
-        / f"team_{runtime.team_id}"
-        / f"exp_{current_exp_id.get()}"
-        / "checkpoints"
-    )
-
-
-def team_path() -> str:
-    runtime = global_runtime()
-    return (
-        Path(runtime.root_path)
-        / "snapshots"
-        / f"org_{runtime.org_id}"
-        / f"team_{runtime.team_id}"
-    )
diff --git a/tests/integration/test_oci_backend.py b/tests/integration/test_oci_backend.py
index 9d215a6..bf76ff4 100644
--- a/tests/integration/test_oci_backend.py
+++ b/tests/integration/test_oci_backend.py
@@ -176,7 +176,7 @@ def test_oci_backend_pull_single_file(artifact, unique_repo):
         # Pull the file
         output_dir = os.path.join(tmpdir, "download")
         result = artifact.pull(
-            repo_name=unique_repo, version="v1", output_dir=output_dir
+            repo_name=unique_repo, version_or_filename="v1", output_dir=output_dir
         )
 
         # Verify file was downloaded
@@ -205,7 +205,7 @@ def test_oci_backend_pull_multiple_files(artifact, unique_repo):
         # Pull the files
         output_dir = os.path.join(tmpdir, "download")
         result = artifact.pull(
-            repo_name=unique_repo, version="v1", output_dir=output_dir
+            repo_name=unique_repo, version_or_filename="v1", output_dir=output_dir
         )
 
         # Verify all files were downloaded
@@ -239,7 +239,7 @@ def test_oci_backend_pull_to_current_dir(artifact, unique_repo):
             artifact.push(repo_name=unique_repo, paths=test_file, version="v1")
 
             # Pull without output_dir
-            result = artifact.pull(repo_name=unique_repo, version="v1")
+            result = artifact.pull(repo_name=unique_repo, version_or_filename="v1")
 
             # Should download to current directory
             assert len(result) == 1
diff --git a/tests/unit/artifact/test_s3_backend.py b/tests/unit/artifact/test_s3_backend.py
index 218bb15..385f81e 100644
--- a/tests/unit/artifact/test_s3_backend.py
+++ b/tests/unit/artifact/test_s3_backend.py
@@ -317,7 +317,7 @@ def test_s3_backend_pull_single_file(s3_client):
         output_dir = os.path.join(tmpdir, "download")
         result = artifact.pull(
             repo_name="org123/team456/exp1/ckpt",
-            version="checkpoint.pt",
+            version_or_filename="checkpoint.pt",
             output_dir=output_dir,
         )
 
@@ -351,7 +351,7 @@ def test_s3_backend_pull_version_folder(s3_client):
         # Pull the version folder
         output_dir = os.path.join(tmpdir, "download")
         result = artifact.pull(
-            repo_name="org123/team456/exp1/ckpt", version="v1", output_dir=output_dir
+            repo_name="org123/team456/exp1/ckpt", version_or_filename="v1", output_dir=output_dir
         )
 
         # Verify all files were downloaded
@@ -385,7 +385,7 @@ def test_s3_backend_pull_to_current_dir(s3_client):
 
             # Pull without output_dir
             result = artifact.pull(
-                repo_name="org123/team456/test-repo", version="test.txt"
+                repo_name="org123/team456/test-repo", version_or_filename="test.txt"
             )
 
             # Should download to current directory
@@ -400,18 +400,18 @@ def test_s3_backend_pull_to_current_dir(s3_client):
 
 
 def test_s3_backend_pull_nonexistent_file(s3_client):
-    """Test pull with non-existent file raises error."""
+    """Test pull with non-existent file returns empty list."""
     from alphatrion.artifact.artifact import Artifact
 
     artifact = Artifact()
 
     with tempfile.TemporaryDirectory() as tmpdir:
-        with pytest.raises(RuntimeError, match="Failed to pull artifacts"):
-            artifact.pull(
-                repo_name="org123/team456/nonexistent",
-                version="missing.txt",
-                output_dir=tmpdir,
-            )
+        result = artifact.pull(
+            repo_name="org123/team456/nonexistent",
+            version_or_filename="missing.txt",
+            output_dir=tmpdir,
+        )
+        assert result == []
 
 
 def test_s3_backend_pull_empty_version_folder(s3_client):
@@ -423,7 +423,7 @@ def test_s3_backend_pull_empty_version_folder(s3_client):
     with tempfile.TemporaryDirectory() as tmpdir:
         # Pull non-existent version folder
         result = artifact.pull(
-            repo_name="org123/team456/exp1/ckpt", version="v999", output_dir=tmpdir
+            repo_name="org123/team456/exp1/ckpt", version_or_filename="v999", output_dir=tmpdir
         )
 
         # Should return empty list
diff --git a/tests/unit/experiment/test_experiment.py b/tests/unit/experiment/test_experiment.py
index 72c8f54..f82720c 100644
--- a/tests/unit/experiment/test_experiment.py
+++ b/tests/unit/experiment/test_experiment.py
@@ -5,9 +5,7 @@
 import uuid
 from datetime import datetime, timedelta
 from functools import partial
-from pathlib import Path
 
-import faker
 import pytest
 
 from alphatrion.experiment import base as experiment
@@ -18,7 +16,6 @@
 from alphatrion.experiment.craft_experiment import CraftExperiment
 from alphatrion.runtime.contextvars import current_exp_id
 from alphatrion.runtime.runtime import global_runtime, init
-from alphatrion.snapshot.snapshot import checkpoint_path
 from alphatrion.storage.sql_models import Status
 
 
@@ -119,25 +116,6 @@ def test_config(self):
                         ),
                     )
 
-
-@pytest.mark.asyncio
-async def test_snapshot_path():
-    team_id = uuid.uuid4()
-    user_id = uuid.uuid4()
-    org_id = uuid.uuid4()
-    init(team_id=team_id, user_id=user_id, org_id=org_id)
-
-    async with CraftExperiment.start(name=faker.Faker().word()) as exp:
-        assert checkpoint_path() == (
-            Path(exp._runtime.root_path)
-            / "snapshots"
-            / f"org_{org_id}"
-            / f"team_{team_id}"
-            / f"exp_{exp.id}"
-            / "checkpoints"
-        )
-
-
 @pytest.mark.asyncio
 async def test_experiment_with_done():
     init(