The best time to prune dwarf apple trees is in late winter or very early spring, before the tree begins to grow and produce leaves. The goal when pruning a fruit tree is to remove any branches that are growing from the main trunk at less than a 45-degree angle. Cut off all branches at a slight downward angle about 1 inch from the main trunk.
Remove any broken or dead branches.
Prune off any branches that are growing or pointing toward the ground.
Cut off any branches that are rubbing against another branch or crossing over another.
Choose one upward-facing branch near the top of the center of the tree to be the central leader. Remove any other branches in the interior of the tree that are growing straight upward.
From the remaining branches, choose five or six evenly spaced around the tree to be the main scaffold branches. These will grow and support lateral branches that will produce smaller spurs from which the apples will form.
Cut back the remaining branches by 1/3 of their length.