If I scan with CCleaner, and it takes away something that I did not want it to, and messes my computer up some how, is there any way to restore it to back to what it was before the scan was run?
No. It's as well you said 'If I scan...' I would run the Cleaner section first with the default settings, it should be harmless. I would also not run the registry clean until I either knew what was being deleted or I had more confidence. Take a registry backup when you do, this part can be restored.