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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.

For small trees, tree removal should take just a couple of hours to complete. Assume that a mid-sized tree will take between four and eight hours, depending on the extent of the equipment required and the health of the tree. Remember to add up to two hours for stump removal. Larger trees could take as long as one or two working days, about eight hours each.

A tree growing close to a house can pose several risks, but removal isn't always the only or best solution. Potential problems include roots growing into the foundation and causing structural cracks, branches damaging the roof or promoting moss growth, and debris clogging gutters, which can lead to water damage. Trees can also provide access for pests and encourage mold. However, a small, healthy tree may not be a problem, and for larger, established trees, strategic trimming can be a cheaper and more beneficial alternative to removal. It is generally recommended to take action for trees within 10 to 20 feet of your home, especially if they are unhealthy or encroaching. Your best bet is to consult a professional arborist who can assess the specific situation and provide expert advice.