BleepingComputer.com: programs folder ransacked

I looked in my programs folder in the computer files this morning and it looks like it's been ransacked. Folders are pushed around and on top of each other--I don't even know where to begin to put them right. How do I and what would do this. The first this I did was a virus scan and it didn't show anything do I downloaded the latest version on my virus software, which has never let me down, and scanned again and still came up with nothing. I've been noticing my computer has been slow and last night my apply button was gone in my Photoshop software. Just odd things that isn't quite right. I also scanned with malwarebytes and didn't come up with anything. Any ideas?