It would help to have a description of exactly what is happening to your system. There are classes of cooties that your computer can have. At the lowest level are simply trackers then there are viruses that can cause operational problems including Windows functions and features becoming corrupt and in the upper level are malware and rootkits.
I suspect that what you are complaining about is actually malware that combines a Trojan and a worm. Malware slips in and replaces a Microsoft file with one of its own, sprinkles the registry with supporting files and then creates the reoccurring pop-up messages from heck. Even if you track down every single file that the malware has created you will be left with the replacement file that has a valid Microsoft name and recently will pass or avoid a Microsoft authentication test. The next time you boot your machine it runs the replacement Microsoft file which then sprinkles the registry and causes the recreation of the bad files again. If this is what you have, hopefully one of the IT guys here can steer you toward a good tool to help you exorcise your machine.
This sort of thing probably explains why I had to get my hard drive wiped and the operating systems reloaded. My problems were kind of like Thompsonian's, with my puter getting bombarded with cookies and some sort of BS fake MS Scan for spyware popups. (Ex-GF admitted to having clicked on one of those at the beginning of this adventure.)
I took it to a good tech who confirmed that I had a bunch of malware infecting the system and explained that even cleaning it once it was on there wouldn't necessarily get rid of the problem. So, the hard drive was wiped, my computer was reloaded, and Webroot's Spy Sweeper was installed to keep viruses, adware, spyware etc. off the machine in the future.
"MS Scan" is a known Malware application. It's nasty...actually downloads a crap load of adware, spyware, etc and won't let you go until you buy it - and then good luck.
Malwarebytes' Anti-Malware 1.24 is free, available at download.com and gets ride of it.
Bitdefender Antivirus has been proven by CNET and other independent sources to be in the top three AV applications. BTW, Norton and McAfee were near the bottom. Free 30-day trial at bitdefender.com and then it's $29.95 for use on up to three computers. Use ZoneAlarm for your firewall instead of the Windows firewall - free and more effective.
Multi-level defense is optimum - Adaware, Spybot, and Spywareblaster (all available at download.com) make a good cocktail. Be sure to update first before you run them.
Finally, after everything has been run and cleaned, do a Registry Clean with Abexo Registry Cleaner and then a defrag with Auslogics Disk Defrag 1.4.16.308 (be sure to go into Setting/Program settings/Defragmentation and choose "Remove Temporary files before defragmentation". Programs are free at download.com.
Open your browser and be sure to go into Internet Options to delete your temporary browser files, too.
Do all your Windows updates.
Then, when you're finished, set a Restore Point.
BTW, I charge $80 an hour for this, and the most you'd spend would be $29.95 and about four hours...
Macintosh !!! 
