There are a number of nail puller bars on the market, I saw at least a half-dozen different ones at Sears. I'd look for one with a tapering width at the nose that can be hammered down to get under the nail head.
In my experience, pole barns are frequently made with green lumber and galvaiized ribbed nails, making nail removal very difficult. I'd be prepared for many of the nail heads to break off before the nail comes out.

If you have access to the underside using a jack to give the panels a little lift makes the job much easier and reduces the damage on the panels. Just a light weight jack and a 2x notched in certain areas to provide support next to the rafters.

Us a couple of C clamps to hold the 2x in place to make it easier snug enough so it doesn't fall. The jack will still be able to lift it the 1//4 to 1/2" you will need to make it easier to grab the head with the puller.

My question would be why do you need to do this? Did someone use aluminum roofing nails on a steel panel or something? Can you just add some self tapping screws if it just needs to be fastened more securely?