Try on Windows' Safe mode by press F8 when Windows start and do virus clean. If you can't boot into Windows anymore, the easier way is that try to copy all data files by whatever methods(HDD->HDD, external USB HDD box....) and then reinstall the new OS la.
For me, if I can go into Windows again, I will backup all data files and then try to use "msconfig.exe" -> Startup to disable any suspected startup files(trojan/virus).