heat gun and reposition would be my vote if they are way off.

a couple notes....

not sure when you say this just how far off they are....if it is less than half a milimeter (e.g., less than half the depth of the veneer) you can just sand it even and not worry about going through the veneer.

if you do go the heat-gun route and haven't done it before....would recommend practicing on a scrap that you glued with epoxy to sort out/get comfortable with temperature/how close you can hold it to the wood/how long.  easy to brown/blacken the wood if you heat it too much.....so would not want to compound the problem with how to take burns off the wood.

all the best

howard

...or, heat a large ziploc bag of water in the microwave to near boiling, then lay the bag across the joint. Wait 5 minutes, and pull the joint apart or reposition and reclamp.

Mas has a Tg of around 132F, and very soft by 148F:

http://www.masepoxies.com/image/5952.gif

   My vote: cover the affected area with a sheet of polyethylene plastic, then put a wet towel, folded in 2 layers, over that. Then use an electric iron. Keep it moving and check frequently. It should get hot enough to soften the epoxy. Then you have two choices: pull the joint apart and start over (messy and persnickety to get all the epoxy out of the joint, and you may need to carefully use a sharp knife or a dremel tool), or press down on the softened joint and try to get it flush. If it does not press easily, use a plastic dead-blow mallet on a piece of wood over the joint. Go for the second option first, and be sure to use a piece of wood as a caul, with a sheet of plastic to prevent the caul from bonding with the softened epoxy in the joint when it's reclamped.

If you intend to finish bright, don't try to sand flush. If you intend to paint, there's no harm in it.

Another option, which I used once when I accidentally put a nasty dent in the surface that would not steam back out, is to dribble successive thin coats of unthickened epoxy over the joint, letting them cure before putting on the next coat. Build up a thick enough covering until you can sand the joint so it appears flush without grinding into the veneer.