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Generally, you should prune around 20% of an apple tree’s growth—and never more than 30%. This means that if you have a severely overgrown tree, it can take a few seasons to prune it back enough to produce the healthiest fruit. 

If you’re dealing with a newly planted or juvenile tree, hold off on pruning beyond the initial shaping. Wait at least a couple of seasons into fruit production since pruning can increase the number of water sprouts and unproductive foliage.

Aside from removing dead or diseased branches, you should prune your trees somewhere between every one and three years. Some people—particularly commercial farmers—prune their apple trees yearly to produce higher yields. This is the best way to promote tree health. That said, the average homeowner can get away with hard-pruning their mature apple tree every other year or every three years. 

Unless there’s some sort of rule in your community’s homeowners’ association that requires you to remove a stump, there’s no law that says you have to take it out. If you’re not wedded to the idea of removing it, there are plenty of ways to get creative with this tree remnant. Using the stump as the medium for a wood carving or turning it into a planter are just two examples of ways to repurpose a tree stump.

Any cutting of tree roots can hurt or kill a tree, which is why it's recommended you don’t do it unless the roots are damaging or invasive on a nearby structure like your home. You should never cut more than 15 percent of above-ground tree roots at one time. If you have any questions about cutting tree roots, contact your local arborist.