After choosing the right tree and carefully planting and watering it, early pruning is one of the most important things you can do for a young tree. If utilizing a tree protector, make sure to remove the lower limbs by simply making a sharp cut where the lateral branch joins the main leader, prior to installation of the tree protector.
Once that is addressed, only dead, damaged or diseased branches should be removed at the time of planting. Seedlings do not need any other pruning. Do not shape the tree, or attempt to balance the branches to the size of the root system. Reducing the leaf area will only further stress the tree, and reduce its capacity for growth.
As your seedling grows out of the top of the tree tube and becomes more established over time, you can prune in late fall, before spring flush or if there are any excessive branches to reduce competition for light, water and nutrients. Make pruning cuts just above an outward-facing bud, and remove branches that rub or are narrowly angled.
Although pruning is essential to good fruit production, be careful not to over-prune, as leaf surface is important for gas exchange and good root production.