I personally use many registry tools, and trust none of them to do 100% of the job. I like cCleaner because at least it is not so aggressive in "cleaning".
In cCleaner->registry->scan for Issues-> Fix selected Issues; at this time you will see a dialog box asking you if you want to back up the registry before the fixing!
I recommend that you read the FAQ for any tools that you plan to use; for cCleaner:
http://www.ccleaner.com/help/faq
cheers ...