diff --git a/apps/cli/executables/pexable/ws_annihilator/ws_annihilator/annihilator.py b/apps/cli/executables/pexable/ws_annihilator/ws_annihilator/annihilator.py
index 06f9fc23d3d75c365324cbc0362cd1c34cd2ebfd..f794ad81ec8b7349b7ef5ffa5e169045beda2b42 100644
--- a/apps/cli/executables/pexable/ws_annihilator/ws_annihilator/annihilator.py
+++ b/apps/cli/executables/pexable/ws_annihilator/ws_annihilator/annihilator.py
@@ -117,6 +117,22 @@ class Annihilator:
         """
         return self._settings.get(area_to_clean.lower())
 
+    @staticmethod
+    def path_valid(constructed_path: str, base_path: str) -> bool:
+        """
+        Check if the constructed path is valid for annihilation
+
+        :param constructed_path: path to verify
+        :param base_path: base path which directory should be annihilated from
+        :return: True if path is valid for annihilation
+        """
+
+        return (
+            constructed_path != base_path
+            and constructed_path != base_path + "/"
+            and len(constructed_path) > len(base_path)
+        )
+
     def get_days_to_keep(self, area_to_clean: str) -> str:
         """
         Return the number of days to keep directories in a specified area from capo settings
@@ -150,7 +166,9 @@ class Annihilator:
         # catch empty string response
         if dir_list:
             for stale in dir_list.split(","):
-                name_list.append(pathlib.Path(str(stale)).stem)
+                # catch empty string directory or whitespace only directory
+                if stale and not stale.isspace():
+                    name_list.append(pathlib.Path(str(stale)).stem)
 
         return name_list
 
@@ -168,7 +186,9 @@ class Annihilator:
         # After annihilation set cleaned flag...
         if area == Areas.SPOOL.value:
             logger.info(f"Annihilation complete for {directory}, setting 'cleaned' flag on workflow request...")
-            self.set_cleaned(directory)
+            path = self.determine_path(area)
+            clean_me = path + "/" + directory
+            self.set_cleaned(clean_me)
         else:
             logger.info(f"Annihilation complete for {directory} in {area}.")
 
@@ -201,15 +221,21 @@ class Annihilator:
 
             for directory in stale:
                 dir_path = path + "/" + directory
-                if not pathlib.Path(dir_path).exists():
-                    if area_to_clean == Areas.SPOOL.value:
-                        logger.info(f"directory {dir_path} not found, setting 'cleaned' flag on workflow request...")
-                        self.set_cleaned(dir_path)
+                if self.path_valid(dir_path, path):
+                    if not pathlib.Path(dir_path).exists():
+                        if area_to_clean == Areas.SPOOL.value:
+                            logger.info(
+                                f"directory {dir_path} not found, setting 'cleaned' flag on workflow request..."
+                            )
+                            self.set_cleaned(dir_path)
+                        else:
+                            logger.info(f"directory {dir_path} not found in {area_to_clean}, skipping...")
                     else:
-                        logger.info(f"directory {dir_path} not found in {area_to_clean}, skipping...")
+                        logger.info(f"found directory {directory}, annihilating...")
+                        self.annihilate_directory(area_to_clean, directory)
                 else:
-                    logger.info(f"found directory {directory}, annihilating...")
-                    self.annihilate_directory(area_to_clean, directory)
+                    logger.error(f"Error: Received invalid directory '{dir_path}' as input for annihilation. Aborting.")
+                    exit(1)
 
     def run(self):
         if self._args.all: