Holes in trees are often unsightly and homeowners may want to patch them up to make the tree look better. They provide homes to pests such as carpenter ants, bees, hornets and wasps, and they can be dangerous if the hole affects the tree structurally. Tree experts don't often recommend patching up a hole. It usually does more damage that can make the tree even more unstable. Small holes are best left alone and structurally unsound trees should be removed. In some instances, however, you can patch trees, like to remove pests from a tree, prevent rain from entering the tree and causing further damage, or supporting a tree until it can be removed.
Fill small holes with a silicone caulking compound so the hole is full until it is flush with the inner layer or bark. Protect the compound from rain if necessary by hanging a tarp above the hole. Leave it in place until the compound is dry or all chance of rain is gone. Compound drying times will vary depending on the manufacturer. This method is often used in holes that were drilled in a tree either to insert an insecticide or to hang an item like a hammock.
Scrape the dead wood from inside a medium-sized hole and fill it with expandable polyurethane foam. This foam will fill the hole, keep moisture out and help support the tree. It works well with trees that have suffered structural damage during a storm. It even works on trees that have had extensive damage but expandable polyurethane foam isn't readily available in large quantities so this method works best in medium holes.
Pour sand into a tree with a large hole that is unstable. Use mortar to seal the opening. This is a traditional method of filling holes in trees but has its disadvantages. The material is coarse and will wear on the inside of the tree, causing further damage. It also doesn't contract, expand and bend like the tree will with different weather conditions, causing further damage.