Regular honeybees do not generally bore into wood or burrow into the ground but yellow jackets do. You can see the difference easily. Yellow jackets are not at all fuzzy and have clearly delineated yellow and dark-brown stripes on their tails. In the ground I have poured motor oil into the hole and this seemed to work.
Regular honeybees do use holes that are already in trees. They make their honeycombs inside.Without knowing if you are talking of a tree or in a home I don't know how to answer. Depending on the damage to a tree, you may need it cut down. Smoke will put bees in a sleep state but this is only temporary. If they are in your house in significant amounts I would suggest an exterminator as bee stings can actually kill you if you get too many, allergic or not.