A small file works fine, or a scraper as Synchro suggested. More importantly is the thorough cleaning. If you do the cleaning yourself, dig into the coolant passages and cavities with a flat blade screwdriver and use a high-pressure pressure washer. Run the pressurized water through all the oil passages. Clean out the oil holes in the crankshaft too, after removing all the plugs, with the pressurized water. The crankshaft will need a bath in solvent to remove all the Cosmoline. After cleaning, spray the block and crank with light oil to protect them from rust. Clean off the outside of the block with acetone before masking and painting.
Don't forget to put all the plugs back in the crank and into the oil passages in the block. Pressure test the block with air to make sure all the plugs are in.
I love my Burtz engine and would get another one if the queen bee would let me buy another Model A.