Cherry trees grow best and yield the most fruit when they are pruned correctly. However, because cherry trees are somewhat delicate and usually only live about 20 years under even the best conditions, you must be very careful when and how you go about chopping off their branches. Cherry trees must be pruned or they will die of starvation, because they cannot support their own unfettered growth, but the actual pruning process should be treated like surgery.
Prune the tree in the summer, after you have harvested the fruit. While most fruit trees are pruned in winter, cherry trees are highly vulnerable to a disease called Silver Leaf that strikes in winter, so it is better to prune them while the weather is still warm.
Cut off any dead or diseased branches. This will help the tree to focus on growing the strong, flourishing branches and prevent diseases and bacteria from sapping the tree's strength.
Remove any smaller seedlings that may be growing at the base of the tree. You can dig these up if you are careful not to injure the main tree's roots, or you can simply cut them off. They cannot stay there, however, because they will die in the shade of the larger tree and sap nutrients out of the soil that the original plant desperately needs.
Cut branches at an angle about 3.2 mm (1/8 inch) above the bud. This will prevent the branch from continuing to grow, but will not threaten the health of the main tree. The angled cut keeps water from sitting on the cut and creating an environment that encourages bacterial infection or disease.
Seal all the pruning cuts with pruning paste or wound sealer. Use a non-asphalt based variety. Pruning paste is like a sticking plaster for trees. It keeps harmful organisms out of the wound while the tree heals.
Unless you have a weeping cherry, try to shape your tree into a "V" shape or an "open vase" configuration. Weeping cherries should be pruned in such a way as to keep their flowing shape.