The best time to prune Japanese Maples is January or early February. December pruning can encourage insects and disease. Pruning too much in one season will cause the tree to produce many small branches at the cuts. You will be fighting these suckering branches for years. The first year, remove the rubbing branches and dead wood. Then prune according to your plan for size and look, never opening large holes in the canopy or removing more than 20% of the tree in one year.