Select dead or diseased branches for pruning. Look for narrow-crotched limbs (narrow in comparison to other sets of limbs.) These are weak branches that may be good targets for pruning.
Select branches and twigs for pruning that lie beyond lateral buds (buds that produce growth in the horizontal plane) or lateral branches in order to achieve a look that will showcase the natural dome-like structure of your tree.
Make diagonal cuts on the selected branches and twigs just past growth-producing buds. Do not cut a branch flush with the trunk. Be sure not to cut into a branch collar – the rounded or ridged areas where the branch meets the trunk. Your Japanese maple will be more susceptible to decay and infection if you damage the branch collar by cutting flush with the trunk.
Inspect your tree for mistletoe or any signs of a borer infestation. Ask a local arborist or your county extension service if there are any known borer infestations in your area that may affect your Japanese maple.
Paint pruning wounds with an asphalt-based pruning seal or tree wound dressing if your tree is afflicted with mistletoe or borers or if there is reason to believe that a borer infestation is spreading to Japanese maples in your area.
If pruning wounds are unsightly, apply a non-toxic sealer as a cover-up. Apply a very light coating of the sealer for cosmetic purposes. Non-toxic substances that can be used for this purpose include latex paint, latex grafting paint, asphalt-based tree wound dressing and silicone-based sealers.