Depends how long you ran the rootkit/virus and how it acted on your system. Best way is a boot device (CD/USB drive, etc..) with a virus/rootkit scanner that can do that. Many new softwares allow for making such CDs. Otherwise if you're going to have a go at it yourself, Safe Mode with no networking is best, unplug NIC from network and any other modems or devices, if internal wireless, block PC name at router.