Linux will format entire hard drive but is BEST to format all before. Make sure you have the linux platform saved as boot in thumb drive at least on a 16gb. If you have anything important make sure you save it on a different thumb drive makes sure not on a floppy disk :P.
Once you are ready to...
I had the same situation in one of my desktops. As soon i open the box it was clogged up, plain dust and thick. I always used air cans to clean the vents but I never open it up. I decided open all apart clean them all, even remove old thermal paste and put a new one. Put everything back in...