C:\WINDOWS\system32\~.exe - Win32.Backdoor.Agent

For quite a while my computer has been making an odd noise,
not the computer itself, but like noise through the speakers.
I’d notice alot when I had headphones on and wasn’t playing
music, very intermittent and then increasing in frequencey, it
sounds almost like Recycle Bin when you delete, rustling paper.

Eventually I decided to go into safemode and do some scans.

Upon doing a scan using AdAware in Safemode, it told me I had a
file in System 32 called “~.exe” (what a wierd name for a file, eh?)
It said it was a backdoor, but to be safe I scanned it with Avast
as well, and it said the same thing, so I put it into Quarantine.

So far my computer is running fine, and no annoying sound…
what is “~.exe” and did it go to anything that was important?

I don’t think it is important… rather, an infection.
You’ve done the correct thing sending it to Chest.
I suggest:

  1. Disable System Restore and reenable it after step 3.
  2. Clean your temporary files.
  3. Schedule a boot time scanning with avast with archive scanning turned on. If avast does not detect it, you can try DrWeb CureIT! instead.
  4. Use SUPERantispyware, MBAM or Spyware Terminator to scan for spywares and trojans. If any infection is detected, better and safer is send the file to Quarantine than to simple delete than.
  5. Test your machine with anti-rootkit applications. I suggest avast! antirootkit or Trend Micro RootkitBuster.
  6. Make a HijackThis log to post here or, better, submit the RunScanner log to to on-line analysis.
  7. Immunize your system with SpywareBlaster or Windows Advanced Care.
  8. Check if you have insecure applications with Secunia Software Inspector.