Similar to the water method LogDog described, you could just scribe it at the desired points and cut..
To cut roots level, set the stump up on the shop floor as you want it to look as your base and brace it in place.
Measure the distance between the floor and the root that is furthest from the floor. Add 3/8" or 1/2" to this measurement.
Cut a piece of 2"x 2" to the dimension you determined above. It is critical that the ends are square.
Tape a pencil to top of of the 2" x 2" that is perpendicular. Check the setup and make sure the pencil is squared up and won't move.
Scribe the stump by keeping the 2" x 2" block fully in contact with the floor while marking a line on the stump.
If you are cutting with a chainsaw, if you use a chisel to mark your line you will get a finished edge and eliminate pullout. Use the chisel to mark the line bevel side toward the cut off edge and flat side to the finished edge, drive it a good 1/2" into the wood (I normally leave the line). If you haven't cut using this method, I would practice on one of the longer roots first to see how close you run the saw to the chisel line.
For the bark, after peeling, a 4" grinder set up with a disc sanding wheel works well for knots and tight spots.