I'm not sure I understand your problem entirely but I will offer what I can.
Get yourself an antivirus like Norton 2005 or Trend Micro that are good at infected file repair. I don't know whether you will need an Enterprise or Corporate level antivirus. You may be able to use a home or home office solution.
But get an antivirus on your computers and run it in safe mode on each system. You might also want to take your individual PCs to an online scan. I recommend McAfee's or BitDefender's online scans.
You might have to run the online scans first provided you can get your computers to the online scans.
If not then you will have to attempt to install the antivirus of your choice on your infected PCs and then run scans.
A few virusses can survive reformats.I don't know whether the virus that hit your Pcs is such a virus.
If it is, you will have to scrub your hard drives and then reformat your disks ( hard drives ).There is a body of thought that once a drive is infected, the only way to secure your system again is to scrub, then reformat your drive. There are a number of good drive scrubbers out there ie. ActiveKilldisk, SecureClean, Cybercide, MediaWipe to name a few.
I hope this helps.
Best of luck to you,