Wendall,
Cougar is right. The only way to flatten it would be to sand it flat. I would be very hard pressed to do this for two reasons. First, I have never worked with mother of pearl or abalone in the "raw". Secondly, the dust produced by these materials are very, very bad for your lungs. I hate to be a wet blanket but unless you know someone that has done this, I would recommend purchasing the mother of pearl scales that are already flattened. Even then, I recommend working with it outside and wearing a good respirator, not one of the paper painter's mask we see at Sears.
CWilkins