If you want to clean up the desktop file of any volume (HardDisk or Floppy) you will fust have to hold down command and option keys before the volume mount (when you restart your mac for HardDisk, or when you insert Floppies fot floppies).
Then a window should appear, asking you if you want to rebuild the desktop.
Say yes, and the ressources of deleted file will be deleted by the system.