Executables won't run after a malware attack

I have had two computers on our network that have been victims of malware attacks. I have run malware bytes and it removes any found threats but executables will not work properly. When clicking on any icon that is not a document, you are prompted with the "Open with" dialog box. I have also used combofix. On the first computer that I encountered the issue with I ended up renaming the user's profile to "user.domain.old". When she logged on next time her profile was recreated and worked fine. Before I do the same to this computer I was hoping for some suggestions.