I'd like to know if there isn't an antivirus or some program of sorts that can actually clean these files.
yes there are....but if you read the blog from Miekiemoes (Assistant Director of Research @ Malwarebytes ) she will tell you why not
http://miekiemoes.blogspot.com/2009/02/virut-and-other-file-infectors-throwing.html
And even though an Antivirus is able to disinfect the files, in a lot of cases, many files will be corrupted anyway > result > many programs won't work > loads of errors > corrupted Windows + there's still no guarantee that the Virus is really gone.
So why bother to clean this if a format and reinstall is the fastest and especially the safest solution?