The first thing to do is find the rattle. Turn up the bass and listen for it to see where it's coming from. When you think you've found it, try holding the part still with your hand to see if it stops. Common sources of rattles are license plates, loose junk laying around the car, and loose bolts and screws. Once you've found it, just tighten the bolt, move the junk, add some foam padding, etc.
A hard top is mostly solid plastic...so I'd probably start at the rear window where all of the moving parts are, and all of the places where the hard top meets the tub.