System Security Virus

Ok. I have finally gotten back to the net. The pop ups are gone but now any program i click comes up with the "open with" box. I do not know how or why the pop ups are gone. As far as I know I did not do anything special. I was able to download malwarebytes but when I click run....you guessed it..."open with". I can not even get regedit to open in safe mode without the 'open with". Does anybody know the next step?