What to do after fake antivirus scam started running?

I got one of those fake anti-virus scam pop-ups on a legit website yesterday (one of those scams that pops up and states that you have a virus on your PC and wants to scan it for errors). When I tried to X out of it instead of pressing OK or cancel, it started running the program. I really quickly hit Ctr-alt-delete to get to my task manager and closed it that way. I ran my own antivirus program after that and it didn't find any infected files or problems. All seems to be okay but today I turned on my PC and noticed weird things like down in my tool bar my icons for things like my wireless connection and my volume are missing. Any ideas on what I should do to see if there are deeper issues that are affected? Thank you!