Virus: apps won't launch (.exe files)

I've run microsoft security essentials, malwarebyt's anti-malware and ccleaner in regular and safe mode and can't seem to pick up the virus/trojan that has disabled all my apps (MS office, firefox browser, MSE, etc.). I can get MSE to run (as administrator). When I launch any app, like microsoft word, I get a window that says "app not found".

I also tried reverting to an earlier restore point, but unfortunately they don't go far enough back prior to the issue.

How can I fix this?

Thank you. Your linked worked perfectly. Yes, I did have a trojan quarantined by MSE but I inadvertently deleted the history. Also, the Update does not work on malwarebytes which, in the past, has been a good indicator of a virus.

I ran malwarebyts again and it picked up

trojan.fakealerts affecting registry value

HKEY_CURRENT_USER\SOFTWARE\Microsoft\Windows\CurrentVersion\Run\3561584484 (Trojan.FakeAlert) -> Value: 3561584484 -> Quarantined and deleted successfully.