What program did you use for that process? My routine is to first do a full/deep scan with a fully-up-to-date antivirus program followed by installing Malwarebytes and a full/deep scan.
As for cleaning the Registry there is only one guarantee
, making the wrong choices in such a program can kill Windows. After having said that, I use CCleaner but then I've used it for several years with only a couple of issues that were quickly fixed by restore to a System Restore Point I had manually created first. CCleaner has the option to do the same.