Hi there

As above you can try to run MB from Scan-Custom Scan and then select HDD which you are suspecting is full of viruses 

Something like this 

Or you can try boot with HDD on which you are suspecting there are viruses and use above SW Combofix or AdwCleaner,I've used both SW and both are very easy to use and they're best,MB is good,but he doesn't remove fully all viruses and all traces 

Sometimes you need to use 2 or more programs to remove all viruses

Hope this help

Thanks,Jura