NIS 2009 disabled

Hello, I hope I’m not being a complete idiot here, but I could really use some help. I believe my computer has become infected with some form of virus or malware. I am subscribed to NIS 2009, but this has stopped working, following an my accidental opening of a pop-up… Although the icons for Live Update and NIS 2009 can still be found in my programs list, they do not launch when clicked. Alongside this, system tools such as disk defrag and system restore refuse to operate. I have run anti-malware software (Malwarebyte’s Anti-Malware) which discovered some infected files and removed them. The problems have persisted. I have also run online malware scanners which failed to find a problem, and repeated uses of Anti-Malware have not uncovered any further infected files. Any help would be greatly appreciated! Thank you.