Another option for your scanning/cleaning of the nasty is to use a LiveCD with an antivirus program. Many of the new trojans set themselves up as a service in Windows and won't let you remove them while running Windows. (It's kinda like changing the spark plugs in your car while driving down the interstate)
I would suggest that you download
Avira AntiVir Rescue System and burn it to a blank CD. the file will be saved as rescue.exe. it's a little over 50 Meg and it should burn itself to CD when you execute it. if not it will ask if you want to save an ISO file. if it doesn't burn it straight out then take this option.
an ISO file is basically an image file of the CD/DVD. soif you don't have an option to "Burn Disc Image" in your CD burning software download
InfraRecorder (also free) and choose "Burn Image" under the "Actions" menu in the top bar.
Using the AntiVir Rescue CD is pretty simple. First you need to reboot the computer and have the CD in the machine. Most machines have the option to change boot order by pressing a Function key (say F12 or something) if the machine isn't already configured to look at the CDRom as an initial boot device.
Once the program starts just hit your Enter key and accept the default. it will start a graphical user environment. once in the GUI click the British flag on the bottom to change the language to English. Then go to "Configuration" and check the two boxes in the middle that say "Try to repair infected files" and "Rename files if they cannot be removed". now click "Virus Scanner" on the left menu to switch to the scanning section. now you are ready to scan the drive.
once it is complete you will see a list of stuff it cleaned or renamed. after looking it over you can exit the program by going to "Miscellaneous" in the left menu and then selecting "Shutdown"
Remove the disc and reboot normally into Windows. once inside Windows go to
Malwarebytes.org and get the free malware scanner. download and run it. also update your antivirus and after the malware scan is complete scan your system with it.
above all have patience. it can be very frustrating, but if you take your time and research the problems you can whip most all the nasties out there without resorting to formatting and re-installing.
also, you can use various LiveCDs to save your data if Windows becomes problematic. it's nice to have the option of popping in a LiveCD, booting the machine, entering a GUI, accessing your "My Documents", and saving the information to an external drive.
good luck getting things sorted.