diff --git a/hokusai/builder.py b/hokusai/builder.py
index c085da8..08774b5 100644
--- a/hokusai/builder.py
+++ b/hokusai/builder.py
@@ -145,6 +145,9 @@ async def _build_single_target(
     provider_index: dict[str, Provider],
 ) -> None:
     """Build a single target by dispatching to the appropriate provider."""
+    # Ensure parent directories exist for targets in subfolders.
+    (project_dir / target_name).parent.mkdir(parents=True, exist_ok=True)
+
     target_cfg = config.targets[target_name]
 
     if isinstance(target_cfg, DownloadTargetConfig):
diff --git a/hokusai/cli.py b/hokusai/cli.py
index f58ad1b..df96bc5 100644
--- a/hokusai/cli.py
+++ b/hokusai/cli.py
@@ -194,12 +194,26 @@ def clean() -> None:
     state_name = state_filename(_project_name(config_path))
 
     removed = 0
+    dirs_to_check: set[Path] = set()
     for target_name in config.targets:
         target_path = project_dir / target_name
         if target_path.exists():
             target_path.unlink()
             click.echo(click.style("  rm ", fg="red") + target_name)
             removed += 1
+            # Track parent dirs that may now be empty.
+            parent = target_path.parent
+            if parent != project_dir:
+                dirs_to_check.add(parent)
+
+    # Remove empty subdirectories left behind, bottom-up.
+    for d in sorted(dirs_to_check, key=lambda p: len(p.parts), reverse=True):
+        while d != project_dir and d.exists() and not any(d.iterdir()):
+            d.rmdir()
+            click.echo(
+                click.style("  rm ", fg="red") + str(d.relative_to(project_dir)) + "/"
+            )
+            d = d.parent
 
     state_path = project_dir / state_name
     if state_path.exists():