The CPU shouldn't make any noise at all, as there are no moving parts in it. That scratching noise can be a couple of things. Since this happens when you open a program, it's probably the hard drive making noise. It could be your hard drive is about to fail. The noise could also mean one of your fans is about to go. I can only suggest taking the side off of your case, listen closely and try to localize where the noise is coming from.
the noise only appears when my cpu usage is over %50, but it sounds like most the noise is coming from the cpu (i thought this was normal so thought nothing of it) although i have a hard drive i cant boot from but can store stuff on it, but its blank, could this be it?
Could be that the CPU fan is cranking up its speed as the temperature increases, and the fan makes that noise at certain fan speeds. You can try manually setting the fan speed in the BIOS and find a speed where it doesn't make a noise. Or you can look at getting a new fan for that cooler, if you think it's dying.
That sounds like the hard drive then. The hard drive is reading data when you open a new program or the start menu. You may want to back up your data if the hard drive is making strange noises. It could very well have something physically wrong with it, and its on its way to failure.
I had this issue with my i5 some time ago, narrowed it down to the PSU (The CPU was making sound though) not delivering the power efficiently to the CPU, got new PSU and sorted the problem other than that on HDDs and Fans can make noise (physically) as said above.