While MWB is good, I would also run Ad-Aware and Spybot S&D when you have had a “partial infection”. Between the three you are pretty well assured that any nasties have been purged, including those that are running.
A big irony is that few of these programs will root out the deepest stuff, that is likely either government installed or advanced hacking. For this you actually have to get counter-hacking software written by hackers. This is very hard to find unless you know the programmer, as getting it off the Internet would be suicidal.
Thank you. I run Comodo, as well.