Whenever there is an alien(virtumonde) infestation:
1. let the local police(KIS) try and handle it
2. when they can't, send in the commandos(HJT) for seek and destroy operations
3. assist the commandos with air strikes(counterspy etc.)
4. if all else fails, then nuke(format) the town(windows) and wipe out the aliens alongwith whatever human residents(data) who were unfortunate enough to have survived the initial infestation and could not be extracted(failed/impossible recovery)
It's been a while since you saw an alien invasion movie hasn't it?
If he is able to end the processes and delete the files, then it may become possible to install antispyware software which could further remove the pest and slowly but surely get back control. Its worth a try before nuking windows.