I messed up my computer when I did a virus scan, please help!

So the other day I got a virus, I ran Malwarebytes and when it was done it had a checked list of what I should delete, so I “Delete all checked” ad when I went to open Google chrome, Skype, Internet Explorer, FireFox, etc. It asked me what I wanted to open it with.
EX: I will double click Firefox and it asks me what I want to open it with, and I click on Firefox, then it opens but something else pops up..

You have chosen to open:
firefox.exe
from C:/Program Files/Mozilla Firefox

Would you like to save this file?
Save file cancel

I click save file and it saves to my downloads as a Firefox application. When I double click to open it it does the same thing. How do I fix this?