The only times I've gotten infections are when I was running AV that was supposed to be able to stop infections from taking place to begin with. Namely, both Symantec and Computer Associate's solutions have both told me (or people working with me) that they stopped an infection, only to find a few days later that the virus has been running all the while. Given that, I've not trusted them, and don't trust any of them.
The bottom line is that if you're working in an environment where you must truly be 100% positive you are secure, there's no real way to recover except a fresh installation. You won't find a security consultant that will disagree.
Yes, for most people, software will fix it all. But the reason that NO AV or Anti-adware app will make a machine as secure as possible is because they only work on definitions and heuristics, which are at best poor. It is easy to go and juggle the WinVNC source and come up with a backdoor for your machine that no one would ever find, and no software would ever remove.
That's why there's no scanners that will make your machine really secure.