Malwarebytes detected a malware program, and after putting it in quarantine my computer won't work right?

I'm using a Toshiba laptop with Windows 7. A Malwarebytes window popped up with a file name and said it was malware and needed to be quarantined or I could choose to leave it alone. I went ahead and clicked quarantine, but now, files can't open. Example: Any program (except Firefox now and Malwarebytes itself) and even some file folders I click bring up a box that says Open With and then has recommended files and other files. The example I'll use is Internet Explorer. When I try to open it, it brings up that box. IE is one of the open with options, but when I click it, it brings up another box that says iexplore.exe run, save, cancel. I chose run first, but IE still won't do anything and the dialog starts again. I chose save once but it said iexplore.exe already exists, overwrite? I did nothing first and then went ahead and overwrote it, but IE is still bringing up the Open With box. Firefox also did this, but after I went into Program Files and clicked the file there, it allowed me to choose Firefox in the Open With box and runs fine. Malwarebytes also did the same thing. I haven't tried anything else, and I really have no idea what's going on. The file that was quarantined I believe had updater in the file name, but I really have no idea what it was. Is there any way to fix this?