I've always used a small ball peen hammer head as a dowel, then hit it with another hammer to flatten out the mushroomed metal. Need to do this on a flat surface, preferably metal.
After you get them flat, take a flat file on run it over the sealing surface to make sure it is flat, but make sure you don't take away too much metal, trans spans are thin !
I've always been told by transmission shops NOT to use RTV on trans pan gaskets.
HINT: when putting the pan & gasket on with no RTV, steal some sewing thread from your wife, and tie the gasket on at several bolt holes to hold it in place. Once you have the bolts in and the gasket snugged up, cut the thread and pull it out (or leave it.....up to you).