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Yes, it is highly recommended to remove tree stumps. Leaving them in the ground can lead to several problems, as they are not only unsightly but can also reduce your property's value. Stumps can obstruct landscaping plans, make mowing difficult, and hinder new growth. More importantly, they are prime breeding grounds for pests like termites, ants, and mice, which can spread to your home and cause costly damage to its wood and foundation. Stumps also attract fungi and diseases that can infect other healthy trees and plants in your yard. As a stump decays, it might sprout new, unwanted shoots. While removing a stump is an investment, it prevents these potential issues and enhances the safety, health, and appearance of your landscape.

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.

It can be bad to leave a dead stump in the ground. A stump becomes a hefty piece of dead wood in time and eventually (especially with the help of rain) starts to rot. That makes it a locus point for diseases and pesky insects, as well as a bit of an eyesore. It’s best to remove a tree stump completely before it starts to decay, especially before it starts to fall apart. If the tree was removed because of disease, it’s even more important to fully remove the stump if possible.

Tree roots are hearty and complex systems, so they don’t die immediately after the rest of the tree is removed. If you leave the root system in place, it takes anywhere from two to seven years for it to run out of nutrients. It is worth noting, however, that the roots stop growing and expanding after cutting down the rest of the tree.