Dress yourself in protective gear to avoid being stung by the honey bees. Your protective gear should include shoes or boots, socks, long, heavy pants, a long-sleeved shirt, gloves and a protective screen-style mask. Ensure you have no skin visible.
Use a flashlight with a red filter to help navigate through your yard at night to access the tree trunk with the honey bees. It's best to deal with a bee problem at night because the insects are dormant at this time, and using a red filter on a flashlight will not alert the bees to your presence.
Spray insecticide specifically designed to kill bees into the tree trunk wherever you can see an opening. If the trunk is rotten, it may contain multiple openings. Spray a liberal dose of the insecticide to kill all of the bees present.
Examine the tree trunk carefully the following morning for signs of bee activity. If some bees are still in the area, wait until nighttime and spray the insecticide into the tree trunk again. Continue this process until the bees are dead or have left the area.