In CCleaner there's an option under the menu 'Registry' called 'Unused File Extension' which (if checked) lists all the filenames for which their extension isn't associated to any application. This should *only* apply to filenames and not to directories. If you have a directory with a dot (say 'test.xyz'), CCleaner will list it among unused file extensions (the unused file extension being 'xyz' of course).
You can test this. Make a directory (or a *folder* in the Microsoft Windows term) named 'test.xyz', access it (double-click the folder) and close it. Then run CClener with the option 'Un