To help a Japanese magnolia grow straight and vertical, prune multiple stems while it is still young enough to leave the dominant trunk. Remove low branches that might become obstructions at the collars against the trunk.
Perform seasonal pruning in late spring to mid-summer after the tree has finished blooming for the year. At this time, cut off any damaged, dead, diseased or infested limbs. Trim branches that rub together or against the tree's trunk, as these might damage the bark and open the tree to disease or infestation. Be sure to cut cleanly against the trunk, making sure to avoid creating shredded or ragged edges.
Though Japanese magnolia trees should be shaped when young and pruned for health, they should be pruned and shaped as little as possible when mature. Pruning cuts in mature trees do not heal easily, and the tree may not be able to recover from the damage. Once a Japanese magnolia tree has matured enough to establish its position and shape, it will live longest if it is left completely on its own.