Lots of times files can't be cleaned -- especially executable files and dlls, I think.
But the virus removal software usually tells you before it deletes the file. Just write down what file it is before you let it get deleted and try to find out what program it was from.
If you have the install program of that particular program you use, you could just reinstall it if it seems not to work. Sometimes the deleted file will make little or no difference if the infected file is of some program that you never use.
I have used Avast! and it works great, but it has a kind of limited library in comparison to Norton Antivirus. I use Norton myself, because I don't want to take any chances with the stuff I have on my hard drive -- that's my livelihood. But I installed it on Heidy's machine and it works just fine.