Normally, you would run the Scan and fix
option when prompted to have check disk
run and attempt to fix any bad sectors and/or file system errors on the removable disk.
You may also need to delete any incomplete files that were being copied to the removable disk if it was removed before finished copying.
If the above fails to fix the removable disk to stop getting the "Do you want to scan and fix....?"
prompt for it, then running the clean
command and formating the removable disk usually will.