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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.

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.

The best plan of action for an unhealthy or unsafe tree will depend on its condition. An arborist can recommend whether trimming or removal is the right call for your tree. Preventive tree trimming can keep trees safe and healthy, so make regular tree trimming a part of your yard maintenance plan.

If tree branches cross well into your property line, in many cases, these branches become part of your property, and you can trim them up until your neighbor’s property line. However, this issue will vary based on local ordinances, so you should do your research before making any decisions. Better yet, speak with your neighbor about how to handle any tree issues. 

If you don’t mind the branches, you can leave them be, but if they’re becoming a hazard, it’s definitely worth having a conversation.