Two wild (naturally) growing small trees have come up in a flower bed close to our home. The roots run rather deep. Do I need to remove the entire root system for the trees in removing them? Thanks
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You don't say if you are trying to save and transplant the tree to another location, or if you just want to kill it as a "weed tree".
If you want to kill it, cut it off at ground level, and immediately spray on or paint on glyphosate weed killer herbicide (i.e., Roundup) directly onto the cut stump of the tree. Do not do this when it is windy, and be very careful not to get the herbicide spray on any nearby flowers, plants or lawn, since it will kill ALL green plants. To help avoid spraying good plants, put a cardboard shield behind the cut stump you are spraying, then don't let the wet shield drip on any plants, or it will kill them. The glyphosate spray will travel down the root of the tree and will kill the root. The chemical is deactivated by the soil, so it does not poison the soil.
If the tree is a black walnut, that is a problem for nearby plants, since walnut trees release juglone chemical, which kills many nearby plants, especially tomatoes and peppers, but also some flowers and shrubs.
On the other hand, if you wish to save and transplant the seedlings, dig a good soil ball about a foot across (or more if the tree trunk is over 1/2 inch) and also a foot deep. Do this when the soil is moist, so the root ball will hold together. Cut the taproot at a one foot depth, and the tree should survive if you replant it immediately and keep it moist, but not sitting in water. March would have been a safer time to transplant, before the tree leaves emerged. Don't fertilize the tree the first year. Replant at the same depth it was growing. Dig a wide hole, but no deeper than the root ball. Mulch with organic mulch, 2-3 inches deep, but never let mulch touch the trunk of a tree.