Animals in your attic can be quite a nuisance, but bats in your attic can cause a lot more trouble than you may be prepared to handle. (The only animals worse than bats in your attic are raccoons and opossums.) When you have some very severe damage to your roof that is caused by bats' droppings and urine, it is more than just a mess--it is a major health concern. To repair your roof and block the bats, here is how this very common and very messy problem is handled.
Bat Exclusion and Clean-up
The first step is to call animal control, since bats are protected and killing them is illegal. The animal control expert will help you exclude the bats from your attack by locating where they are coming in, waiting for them to leave, and blocking their entrances. There are also special exclusion nets which can be placed over their exits. The nets allow the bats to leave the attic, but prevent the bats from re-entering. Then the animal control specialist can clean all of the bat feces out of your attic and neutralize the ammonia from the urine and the histoplasmosis from their feces (with a fungicide) so that the roofers can begin their work.
Roof Tear-off and Rebuild
Since the bat urine has undoubtedly left your home with many weakened and rotting timbers, most roofers will only opt for a complete roof tear-off and rebuild job. This means that everything, including the trusses, will have to go. It is removed and deposited into dumpsters or a dump truck waiting below. Your ceiling in the second story of your home (if applicable) may be affected, and you may want to room downstairs for a while or find some other place to board for a week or two. Once your new roof is on, the bats will be fully excluded because the new roof will have no place for them to enter and roost--your roofing contractor will make sure of that.
Check Nearby Structures
Bats of a similar kind are drawn to each other by the pheromones they leave in their urine. If they filled out your attic, they may also have been drawn to the rafters of other structures. Be sure to check your garage, shed, etc. for signs of bats there too. Otherwise you might have to repeat this whole process with another visit from wildlife control and another roof tear-off and rebuild project.