To prune a mature apple tree, cut dead, diseased and damaged branches off near the trunk, and remove any shoots growing on the base of the tree. Cut away the vertical shoots growing on the main branches of the tree, and thin the fruit-bearing branches out so that they are evenly spaced. Remove branches that are competing by cutting of the weaker branch where the branches fork at the tree trunk.
When pruning a young apple tree, locate the center branch, and pinch back all other branches during the first summer. During the tree's first winter, thin branches into layers that are four inches apart vertically to create a scaffold-appearance, and prune the tree into a pyramid shape with the center branch as the tip of the pyramid.
Continue scaffolding the branches in the second and third winters, or until the tree has three to four sets of layered branches. After the tree has three to four layers of branches, allow the bottom branches to grow longer than the top branches to maintain the pyramid-shape of the tree.
When pruning neglected, mature apple trees, cut away all weak branches, and remove shoots growing vertically on the branches and tree trunk. Thin the branches to those with the best angles over the course of three to four years.