It’s best to start shaping early, 2 or 3 years after planting, and prune a little each year. If you start early and prune annually, rarely will you have to cut any branches too large for hand pruners.
Prune a Japanese maple when leaves are gone, the tree is dormant, and the branch structure is clearly visible, or in early summer, when it’s easier to tell dead wood from live wood and to judge the artistic effect. Don’t prune from late winter through spring, when the sap is running. Sap oozing from pruning wounds is unsightly and can attract fungal diseases.
First identify the ideal form of the particular cultivar, so you know what you are aiming for. Is it intended to be upright? Vase-shaped? Horizontally branched? Weeping?
Make sure pruners are clean and sharp. As with any tree or shrub, first cut out all dead wood, especially from the interior of mounded varieties for better air circulation.
Then look for branches that are rubbing each other or that, if left to grow, will run into each other or block each other’s sunlight. Keep the one that will contribute most to a pleasing shape and cut the other back to the next branch, just outside the branch collar.
The rest of pruning aims to balance the plant and accentuate its intended form. If it is a weeping variety, take out renegade branches that head up. If it’s upright, take out branches that grow downward. If it’s horizontal, take out anything too vertical. In other words, prune to enhance the natural habit. If it’s lacy, take out dense growth to so that light can emphasize the leaf form. If the bark is a special feature, make sure it’s visible. If the tree is lopsided, even it up—unless the offbeat effect is artistically appealing, but even so, aim for balance.
Prune with restraint. Step back often and consider the effect. When in doubt, err on the side of leaving the rest for next year.