so, a few days ago, I had a weird advertisemant pop up over my window, (accually in my window) covering the entire webpage, though it had a skip button, I've ben dealing with this every once in a while up untill now, Now it is coming up at every webpage I open, (i.e. youtube facebook even bethesda, and other forum sites.) I have the free microsoft anti-virus software and I ran a full scan and it said everything was fine, I have cleaned my temp files and cookies. Now I have no clue what I should do...... so now defeated, I came to you, to ask for help.
Anti-virus scanners are almost useless after infection, unless they detect the malware and quarantine it. Dedicated malware cleaner are much more effective in cleaning systems after infection.
Try scanning with MBAM, (link): http://www.malwarebytes.org/
However, if you have infected by a Trojan, it can be very difficult to completely remove it. Trojans themselves can infect you with other malware causing a loop of multiple infections.
edit: Wow I need to post more quickly