Runoutofnames

Hi- I have read the posts about using CCleaner on an external HD, but I still have questions. I have a HD that was badly infected with viruses, cleaned it up with my antivirus prog, and now I'd like to do the registry cleanup. When I select a file for the cleaner to clean I get a warning message that it will delete ALL files when it's done. Does this mean everything, or just the crap? Thanks