Bicycle Mechanics - disc brake issue

I have shimano deore hydraulic brakes on my stumpjumper (hardtail) whenever i try to feather the rear brakes they make the most horrible noise and vibrate the entire bike. I was wondering if they are merely breaking in or if i have a problem.

You have a problem. First check and make sure all the hardware is tight. Don't wring anything off, if you start finding loose screws(esp. the rotor bolts) get a torque wrench and check everything.
With the wheel out check the pads to make sure they are not worn out. Some of the deore pads wear pretty quick
Another issue could be contamination. Clean the rotor with rubbing alcohol, if the pads appear to be contaminated replace them.

ok
1. all of the bolts are tight.

2. I took the bike to LBS and they also mentioned that the pads might be contaminated, so they cleaned them and that helped until I took it to the trail and it just started up again.

3. The rotors are slightly "streaked" so i will try to clean them and see what happens, thanks for the help.

how do I tell if the pads are contaminated?
and thanks again you're more helpful than the bike store and i've spent over $1300 there.

Did this bike have the brakes bled? If so I bet the pads were not removed and have been contaminated. It can be hard to tell if they are. Sometimes you can tell just by pulling them out and looking at them. If in doubt just replace them. You either take out a threaded pin or cotter pin, slide the pads out and install new ones(With the return spring installled) Be sure to clean the rotor good before you put the new pads in.

do you recomend any good brake pads? i have deore 525s.

maybe your rotors are warped..?