diff --git a/cmd/gh-aw/main.go b/cmd/gh-aw/main.go
index cc5873f038..c27834153a 100644
--- a/cmd/gh-aw/main.go
+++ b/cmd/gh-aw/main.go
@@ -49,7 +49,7 @@ For detailed help on any command, use:
 }
 
 var newCmd = &cobra.Command{
-	Use:   "new [workflow-base-name]",
+	Use:   "new [workflow-id]",
 	Short: "Create a new workflow Markdown file with example configuration",
 	Long: `Create a new workflow Markdown file with commented examples and explanations of all available options.
 
@@ -63,10 +63,14 @@ When called with a workflow name, creates a template file with comprehensive exa
 - Tools configuration (github, claude, mcps)
 - All frontmatter options with explanations
 
+The workflow-id is the basename of the markdown file without the .md extension.
+You can provide either the workflow-id (e.g., 'my-workflow') or the full filename (e.g., 'my-workflow.md').
+
 Examples:
   ` + constants.CLIExtensionPrefix + ` new                      # Interactive mode
   ` + constants.CLIExtensionPrefix + ` new --interactive        # Interactive mode (explicit)
   ` + constants.CLIExtensionPrefix + ` new my-workflow          # Create template file
+  ` + constants.CLIExtensionPrefix + ` new my-workflow.md       # Create template file (alternative format)
   ` + constants.CLIExtensionPrefix + ` new issue-handler --force`,
 	Args: cobra.MaximumNArgs(1),
 	Run: func(cmd *cobra.Command, args []string) {
@@ -105,8 +109,16 @@ Examples:
 }
 
 var removeCmd = &cobra.Command{
-	Use:   "remove [pattern]",
+	Use:   "remove [workflow-id-pattern]",
 	Short: "Remove workflow files matching the given name prefix",
+	Long: `Remove workflow files matching the given workflow-id pattern.
+
+The workflow-id is the basename of the markdown file without the .md extension.
+You can provide a workflow-id prefix to remove multiple workflows, or a specific workflow-id.
+
+Examples:
+  ` + constants.CLIExtensionPrefix + ` remove my-workflow       # Remove specific workflow
+  ` + constants.CLIExtensionPrefix + ` remove test-             # Remove all workflows starting with 'test-'`,
 	Run: func(cmd *cobra.Command, args []string) {
 		var pattern string
 		if len(args) > 0 {
@@ -125,9 +137,13 @@ var enableCmd = &cobra.Command{
 	Short: "Enable agentic workflows",
 	Long: `Enable one or more workflows by ID, or all workflows if no IDs are provided.
 
+The workflow-id is the basename of the markdown file without the .md extension.
+You can provide either the workflow-id (e.g., 'ci-doctor') or the full filename (e.g., 'ci-doctor.md').
+
 Examples:
   ` + constants.CLIExtensionPrefix + ` enable                    # Enable all workflows
   ` + constants.CLIExtensionPrefix + ` enable ci-doctor         # Enable specific workflow
+  ` + constants.CLIExtensionPrefix + ` enable ci-doctor.md      # Enable specific workflow (alternative format)
   ` + constants.CLIExtensionPrefix + ` enable ci-doctor daily   # Enable multiple workflows
   ` + constants.CLIExtensionPrefix + ` enable ci-doctor --repo owner/repo  # Enable workflow in specific repository`,
 	Run: func(cmd *cobra.Command, args []string) {
@@ -144,9 +160,13 @@ var disableCmd = &cobra.Command{
 	Short: "Disable agentic workflows and cancel any in-progress runs",
 	Long: `Disable one or more workflows by ID, or all workflows if no IDs are provided.
 
+The workflow-id is the basename of the markdown file without the .md extension.
+You can provide either the workflow-id (e.g., 'ci-doctor') or the full filename (e.g., 'ci-doctor.md').
+
 Examples:
   ` + constants.CLIExtensionPrefix + ` disable                    # Disable all workflows
   ` + constants.CLIExtensionPrefix + ` disable ci-doctor         # Disable specific workflow
+  ` + constants.CLIExtensionPrefix + ` disable ci-doctor.md      # Disable specific workflow (alternative format)
   ` + constants.CLIExtensionPrefix + ` disable ci-doctor daily   # Disable multiple workflows
   ` + constants.CLIExtensionPrefix + ` disable ci-doctor --repo owner/repo  # Disable workflow in specific repository`,
 	Run: func(cmd *cobra.Command, args []string) {
@@ -262,8 +282,12 @@ The workflows must have been added as actions and compiled.
 This command only works with workflows that have workflow_dispatch triggers.
 It executes 'gh workflow run <workflow-lock-file>' to trigger each workflow on GitHub Actions.
 
+The workflow-id is the basename of the markdown file without the .md extension.
+You can provide either the workflow-id (e.g., 'daily-perf-improver') or the full filename (e.g., 'daily-perf-improver.md').
+
 Examples:
   gh aw run daily-perf-improver
+  gh aw run daily-perf-improver.md   # Alternative format
   gh aw run daily-perf-improver --repeat 3  # Run 3 times total
   gh aw run daily-perf-improver --enable-if-needed # Enable if disabled, run, then restore state
   gh aw run daily-perf-improver --auto-merge-prs # Auto-merge any PRs created during execution`,
diff --git a/pkg/cli/commands.go b/pkg/cli/commands.go
index c7c3cc1256..5912f7d6d3 100644
--- a/pkg/cli/commands.go
+++ b/pkg/cli/commands.go
@@ -106,6 +106,11 @@ func resolveWorkflowFile(fileOrWorkflowName string, verbose bool) (string, error
 func NewWorkflow(workflowName string, verbose bool, force bool) error {
 	commandsLog.Printf("Creating new workflow: name=%s, force=%v", workflowName, force)
 
+	// Normalize the workflow name by removing .md extension if present
+	// This ensures consistent behavior whether user provides "my-workflow" or "my-workflow.md"
+	workflowName = strings.TrimSuffix(workflowName, ".md")
+	commandsLog.Printf("Normalized workflow name: %s", workflowName)
+
 	if verbose {
 		fmt.Printf("Creating new workflow: %s\n", workflowName)
 	}
diff --git a/pkg/cli/commands_test.go b/pkg/cli/commands_test.go
index 029e8c2b10..4ad1be30d5 100644
--- a/pkg/cli/commands_test.go
+++ b/pkg/cli/commands_test.go
@@ -569,6 +569,12 @@ func TestNewWorkflow(t *testing.T) {
 				}
 			},
 		},
+		{
+			name:          "create workflow with .md extension (should normalize)",
+			workflowName:  "test-with-ext.md",
+			force:         false,
+			expectedError: false,
+		},
 	}
 
 	for _, test := range tests {
@@ -590,7 +596,9 @@ func TestNewWorkflow(t *testing.T) {
 
 			// If no error expected, verify the file was created
 			if !test.expectedError {
-				filePath := ".github/workflows/" + test.workflowName + ".md"
+				// Normalize the workflow name for file path (remove .md if present)
+				normalizedName := strings.TrimSuffix(test.workflowName, ".md")
+				filePath := ".github/workflows/" + normalizedName + ".md"
 				if _, err := os.Stat(filePath); os.IsNotExist(err) {
 					t.Errorf("Expected workflow file was not created: %s", filePath)
 				}
@@ -607,7 +615,7 @@ func TestNewWorkflow(t *testing.T) {
 						"on:",
 						"permissions:",
 						"safe-outputs:",
-						"# " + test.workflowName,
+						"# " + normalizedName,
 						"workflow_dispatch:",
 					}
 					for _, element := range expectedElements {
diff --git a/pkg/cli/logs.go b/pkg/cli/logs.go
index 52ff64d572..027193272c 100644
--- a/pkg/cli/logs.go
+++ b/pkg/cli/logs.go
@@ -312,11 +312,12 @@ Downloaded artifacts include:
 - workflow-logs/: GitHub Actions workflow run logs (job logs organized in subdirectory)
 
 The workflow-id is the basename of the markdown file without the .md extension.
-For example, for 'weekly-research.md', use 'weekly-research' as the workflow ID.
+You can provide either the workflow-id (e.g., 'weekly-research') or the full filename (e.g., 'weekly-research.md').
 
 Examples:
   ` + constants.CLIExtensionPrefix + ` logs                           # Download logs for all workflows
   ` + constants.CLIExtensionPrefix + ` logs weekly-research           # Download logs for specific workflow
+  ` + constants.CLIExtensionPrefix + ` logs weekly-research.md        # Download logs (alternative format)
   ` + constants.CLIExtensionPrefix + ` logs -c 10                     # Download last 10 matching runs
   ` + constants.CLIExtensionPrefix + ` logs --start-date 2024-01-01   # Download all runs after date
   ` + constants.CLIExtensionPrefix + ` logs --end-date 2024-01-31     # Download all runs before date
diff --git a/pkg/cli/update_command.go b/pkg/cli/update_command.go
index a899dc67c5..0c1d25ab35 100644
--- a/pkg/cli/update_command.go
+++ b/pkg/cli/update_command.go
@@ -35,9 +35,13 @@ For workflow updates, it fetches the latest version based on the current ref:
 - If the ref is a branch, it fetches the latest commit from that branch
 - Otherwise, it fetches the latest commit from the default branch
 
+The workflow-id is the basename of the markdown file without the .md extension.
+You can provide either the workflow-id (e.g., 'ci-doctor') or the full filename (e.g., 'ci-doctor.md').
+
 Examples:
   ` + constants.CLIExtensionPrefix + ` update                    # Check gh-aw updates and update all workflows
   ` + constants.CLIExtensionPrefix + ` update ci-doctor         # Check gh-aw updates and update specific workflow
+  ` + constants.CLIExtensionPrefix + ` update ci-doctor.md      # Check gh-aw updates and update specific workflow (alternative format)
   ` + constants.CLIExtensionPrefix + ` update ci-doctor --major # Allow major version updates
   ` + constants.CLIExtensionPrefix + ` update --pr              # Create PR with changes
   ` + constants.CLIExtensionPrefix + ` update --force           # Force update even if no changes