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Though it will be different based on each situation, average costs for dealing with a bat colony in a home ranges from $400 to over $9000 for very large or extensive infestations. Commercially, these costs can run even higher based on several factors such as the height of structures and accessibility. Bat removal can be tedious because it takes attention to detail to make sure every possible entry is sealed before the main entry areas have one-way valves installed to remove the animals and prevent them from entering a new spot. The clean-up portion can be equally challenging when it requires the removal of building materials to access the guano hidden where the bats resided.