Bob Tilden , Feb 22, 2009; 06:37 p.m.
You probably don't want to flatten it- the emulsion may crack and/or come off.
If you -really- need to use the scanner then consider combining several scans, start with two scans at 90 degrees from one another. If you are using photoshop you can play with layer combinations of the two- 'darken' may be what you're looking for...
You may also be able to get a good result by photographing the plate and playing with the lighting angles. If it's really importent to get a reflection-free image then polarizing the lights and a cross polarizer on the lens will get rid of most of the specular reflections.