Answer: The best time to prune Japanese Maples is January or early February but there is still time to do it now. 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. It is better to break major pruning into a three-year plan. The first year, remove the rubbing branches and dead wood. Then prune according to your plan, never opening large holes in the canopy or removing more than 20% of the tree in one year.
Take your time! Stop often to survey the effects of your pruning. Always evaluate each angle of view before a major cut. Spend time studying the new shape, size, and view. You can always cut more, but you can't put it back on once cut!
Modern pruning methods call for cuts just above the branch collar (the raised ring where the branch meets the trunk) and discourages painting cuts. Japanese Maples are an exception! Leave a stub above the branch collar. The stub can be removed after it has died back to the collar. Seal all cuts larger than a pencil with wax-based paste (I have used Elmer's glue in a pinch). Not following this procedure can result in die-back and rot into the main trunk causing decline and eventual death of the tree.
In late spring and early summer after the trees have leafed out, they can be lightly pruned to produce a cloud effect by separating the foliage into cloud-shaped masses along the trunks.
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