turn off the computer
boot into safe mode (press F8 like a crazy person during boot up, and then select Safe Mode when given the option)
run Malwarebytes, and any other antivirus software that you may have
run 'msconfig' and deselect everything except for Windows, your antivirus, and other things you want to run (like special mouse, graphics, or other hardware related software) (start, run, msconfig, startup tab)
reset the computer in safe mode again, and run a full scan of all your antivirus/antimalware software again, repeat this until you get a clean scan
reset again, and go into normal windows, check for antivirus updates, and scan again
run CCleaner's Cleaner, and registry check to remove registry entries related to the malware that has been removed. Rerun the registry checker until you are clear, or there is 1-2 items that it cannot fix.
hope and pray that everything was found
install a physical firewall (like a router) that can run Tomato or DD-WRT which will automatically block most malware attacks, never let your antivirus go out of date, and never ever download or click on anything that could possibly be suspicious.
Estimated time: 6-24 hours depending on how badly infected you are.
Find your restore/install discs and pray that you have backups of all your important files on some other device
During the windows install process be sure to delete your Windows partition (careful not to delete your recovery partition if your recovery disc is on your HDD), and then reformat it which will wipe away all but the most evil boot sector or Bios viruses.
Reload Windows and all your programs.
Get a good router that can run Tomato or DD-WRT to prevent most future attacks
Install antivirus as soon as Windows is up, and before doing any updates or other installations.
Estimated time: 3-6 hours, and you can rest assured that the bug is gone (unless it is a boot sector virus, which means you have to run something like DBAN. Or a BIOS virus in which case you have to flash your BIOS or get a new mobo... both of these are EXTREMELY rare though.)
Also, while Malwarebytes is really really good (I use it on ~300 systems that I am responsible for, and it is an invaluable tool), it is still no substitution for an antivirus program.
I highly suggest Microsoft Security Essentials, but there are other excellent free antivirus programs out there like AVG Free, or Avast! Free. But do not run more than one antivrus program on your system at the same time as they will fight each-other for resources without adding much extra security. Just pick one antivirus, and one anti-malware program (MSE just added an antimalware component, but I am not sure how effective it is yet, but I am hoping it will replace Malwarebytes).