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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.

Your neighbor is not in a good position to know if your trees are truly dead or pose any kind of danger. That’s why hiring an arborist or tree service expert can be such an important part of the process. If the trees are still alive and don’t pose any threat, you’re in the clear (but you may want to document and photograph everything in case events turn sour down the road).

But if a tree is visibly dead and near the property line, you should remove it to be safe. If a dead tree falls on a neighbor’s property, they may have grounds to sue for negligence. If any branches on trees have died, it’s a good idea to cut them back for similar reasons.

Generally, you’ll want to prune back the trunk by 1 to 2 feet each year to promote bushy growth. Doing so concentrates vegetative buds closer to the bottom of the tree, where you can easily harvest fruit. For side shoots that are a year old, leave at least six leaves. 

Never remove more than 30% of a tree’s foliage during pruning—even if your tree is really overgrown. Removing this much foliage at a time could kill your tree.

Surface-level tree roots might only pose a small threat, such as being a tripping hazard or obstacle when you mow your lawn. But if mature tree roots start growing in the direction of your home’s foundation or plumbing system, it could be a real problem. Cutting small tree roots out before they grow too large can keep your home safe without removing the whole tree.