diff --git a/fre/run/workdir.py b/fre/run/workdir.py
new file mode 100644
index 000000000..d29db03ba
--- /dev/null
+++ b/fre/run/workdir.py
@@ -0,0 +1,25 @@
+# ---------------- set up working directory structure
+# Need to import variables: workDir, tmpOutputDir
+from pathlib import Path
+import os
+import shutil
+import sys
+
+workDir = Path("/path/to/directory")
+
+if workDir.is_dir():   #checks for existence and if path is directory
+  if os.access(workDir, os.R_OK | os.W_OK):  #checks read and write permissions
+    for item in work_dir.iterdir():
+      #remove everything except temporary directory
+      if item == tmp_output_dir: 
+        continue
+      try:
+        # Delete all files, folders, and links
+        if item.is_file() or item.is_symlink():
+            item.unlink()  # Deletes individual files or symlinks
+        elif item.is_dir():
+            shutil.rmtree(item)  # Recursively deletes directories (rm -rf)
+            
+    except Exception as e:
+        # Incase of a weird glitch, error instead of crash
+        print(f"Skipped {item} due to error: {e}")