Prune out dead, damaged or diseased branches any time of year when you see them. Cut dead branches back to the base of the branch, making the cut just outside the branch collar, which is the ridge of bark that forms at the joint where the branch meets the trunk or a main branch. Cut damaged or diseased branches back at least 6 inches into healthy wood, making the cut just outside a leaf, bud or lateral branch. Alternatively, you can remove the entire branch.
Watch for improperly growing branches as the crape myrtle grows. In the spring, remove any branches that grow across another branch or inward toward the center of the tree. Cut the branch just outside the branch collar. Removing these branches will produce a stronger structure as the tree matures and increase the air circulation in the canopy.
Train your multi-trunked "Muskogee" to grow with a single trunk if desired. Beginning when the tree is planted, remove all but the strongest trunk back to the base of the tree. Continue removing any new growth that emerges from the ground yearly as the tree grows.
Prune the canopy yearly to reduce the overall size if the "Muskogee" grows too large for its location. Cut the ends of the main branches on the outer portion of the canopy back to a lateral branch. The lateral branch should have a diameter at least one-third the size of the portion being removed. Make cuts just outside the branch collar. Lateral reduction pruning will help retain the natural shape and look of the tree.
Remove lower branches in the canopy if desired as the tree matures to expose more of the attractive bark of the trunk and make it easier to mow or walk beneath the tree.