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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.

If you aren’t sure what you’re doing, be very careful when cutting mature tree roots (roots larger than 2 inches). Root cutting and pruning can affect both a tree’s stability and its ability to nourish itself. Issues during root cutting can result in damage or injury. 

It’s recommended you call in a pro to help, unless it’s a very small tree and you aren’t worried about the prospect of losing the tree.

In most cases, you should not use a pruning seal on trees after trimming. Applying a sealant can interfere with the tree's natural healing process, and it does not guarantee protection from pathogens. Instead of sealing the cut, the best practice is to support the tree's natural recovery by providing it with plenty of water and a dormant-style fertilizer. However, there are exceptions. Pruning seals may be recommended for very vulnerable species, like elm trees, in areas where dangerous diseases such as Dutch elm disease are prevalent. In these specific situations, the protection offered by a sealant can outweigh its downsides. For advice tailored to your situation, especially after cutting large branches, it is best to consult a local tree trimming professional.

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.