You can sill use Medicare to create the USB and then add your favorite antimalware rescue CD to it, like the Kaspersky/Avira ones, but if it’s an unknown malware you’d have to use other analysis tools like Sysinternals RootkirRevealer, Autoruns etc. If you want to fix Windows stuff then it’s best to get a WinPE-based live CD with these tools, like Sergei Strelec, Gandalf etc.