The easiest thing to do here would be a system restore. If this happened lately try restoring to a previous date when you think the computer was working fine. Get into safe mode first to do this.
If it doesn't work in safe mode, then launch safe mode with command prompt. When you get the command prompt type this in: "c:\windows\system32\restore\rstrui.exe" and press enter. That is the command line for system restore. And just to be sure restore to a date maybe 2-3 days ago.
Once the restore is successful, download and run Malwarebytes : Free anti-malware, anti-virus and spyware removal download
. Do a full scan. It should be able to detect anything that might have bypassed Microsoft Security Essentials.
You could always do those other steps suggested by other people like running (rkill, combofix, etc) but there are just too many steps to do. A system restore usually does the trick as I always do this for people at work who get fake anti-viruses and resolve them 90% of the time. Then I download and run Malwarebytes just to make sure there is nothing else on the system.