PC riddled w/unfindable malware

I can't get rid of malware that can't even be found. Something has put false subfolders on every folder on my system. This is the second time I've had this infection. Last time, there were so many errors for Windows Scandisk to fix that I just let it fix them all automatically.

BIG mistake. The result was that virtually every file on my system got truncated. Everything had to be reinstalled, including Windows, but the worst of it was the multitude of documents whose original names may never be put back. To give a new name, I'd have to read each one. The automatic "fix" by scandisk "fixed" almost 100,000 files on C: and half as many on D:.

Now it's back. I'm not ABOUT to let scandisk fix them automatically, and it would take a year to fix each one individually - and the file names would still end up truncated.

It goes like this: Scandisk, on reboot after any crash or power failure, finds "directories" that it says are not usable. In each case, there IS no such folder. These folders all have two-digit names, like Be or a letter or number plus a winging, or sometimes two wingdings. The parent folders to these nonexistent folders continue to be functional. UNTIL I try to have scandisk fix one or more of them.

So it has gotten into my system TWICE. Right past either Avast! or AVG, and right past ZoneAlarm Pro. Nothing stops it from entering. Nothing can find it once it's in my system, including S&D. I have to wonder if these "security" programs are worth anything at all.

If somebody recognizes this infection and can advise me, I'd be deeply grateful. Malware that you KNOW is on your system, but which cannot be found is malware that will return if you ever get rid of it.

This malware has survived several complete formats of C:. If that can't get rid of it, what can? I imagine it must be lurking in BIOS somewhere, or perhaps in the segment of the registry that is NOT erased by a format of C:. In which case, I'm still SOL, aren't I?

I could, and probably will, use a total disk wiper that zeroes out everything on the HD, but I don't know how I'd get the BIOS up and running after that. And I'll still get it back again, as I've already had it twice.

This is just ONE of several infections. I'm being hacked, too - one creep attempted to open a file called "E-mail and passwords," but it was a Word document under a password; Word hadn't yet been installed. Windows notified me it couldn't be opened. I had NOT tried to open it. But that's another story. I left the hacker a love letter; I transferred the contents of that file to a new file, and wrote a scathing/threatening note to the hacker on the original file. I hope he opened it and "made" in his drawers.

One nightmare at a time is best, though.

Can anyone help with this phantom-folder phenomenon?