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I was able to cut out my toilet flange and put a new one in at the proper height. I tried the reaming tool that was suggested above, but the size that someone recommended I buy was not the correct size. I cut mine out using a reciprocating saw--if you do this, go slow and be very careful not cut the drain line. You could probably also use a hand saw. I cut off the top of the flange and then made a vertical cut along the side wall of the flange. Once I cut through the side wall of the flange I carefully used a chisel to separate the flange from the drain pipe. I put a rag down into the drain pipe to prevent pieces of the flange from breaking away and dropping into the pipe
This would be the correct to address this problem. Good luck, tom