diff --git a/lib/main.py b/lib/main.py
index 6355b06..703b5a3 100644
--- a/lib/main.py
+++ b/lib/main.py
@@ -24,6 +24,8 @@
 from lib.common import WitUserError, error
 from lib.gitrepo import GitRepo
 import re
+from glob import glob
+import pathlib
 
 log = getLogger()
 
@@ -71,6 +73,11 @@ def main() -> None:
 
     subparsers.add_parser('fetch-scala', help='Fetch dependencies for Scala projects')
 
+    clean_parser = subparsers.add_parser('clean', help=('delete non-package subdirectories '
+                                                        'in your workspace'))
+    clean_parser.add_argument('--dry-run', dest='dry_run', action="store_true",
+                              help='do a dry run, showing what would have been deleted')
+
     args = parser.parse_args()
     if args.verbose > 3:
         log.setLevel('TRACE')
@@ -129,6 +136,9 @@ def main() -> None:
 
             elif args.command == 'fetch-scala':
                 fetch_scala(ws, args, agg=False)
+
+            elif args.command == 'clean':
+                clean(ws, args)
         except WitUserError as e:
             error(e)
 
@@ -319,3 +329,24 @@ def version() -> None:
         version = re.sub(r"^v", "", version)
 
     print("wit {}".format(version))
+
+
+def clean(ws, args) -> None:
+    subdirs_str = glob(str(ws.path)+'/*/')
+    subdirs = [pathlib.PosixPath(f) for f in subdirs_str]
+
+    pkg_folders = [pkg.get_path() for pkg in ws.lock.packages]
+
+    non_pkg_folders = [f for f in subdirs if f not in pkg_folders]
+    if not non_pkg_folders:
+        log.info("No non-package directories found.")
+        return
+
+    if args.dry_run:
+        log.info("Skipping execution because of --dry-run. Would have run:")
+
+    for folder in non_pkg_folders:
+        if args.dry_run:
+            log.info("rm -rf {}".format(folder))
+        else:
+            folder.rmdir()