1. Trap them using a live trap. Live traps are where you catch them "a live." Only problem is getting rid of them.
2. Call an exterminator or someone who can do the work for you. They have the experience, the equipment and know best how to do it, but they will cost you some money.
3. Use a powerful strobe light. Squirrels and other animals that might inhabit your roof have very sensitive eyes and are easily bothered by this flashing light.
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You can use a Havahart trap, which you may be able to borrow from your County Animal Control officer. He will take the trap with raccoon, and release the raccoon in the woods. http://www.havahart.com/store/live-animal-traps/target-animal/raccoon
Look for the way that they got in and wait till they go out to look for food then block the hole. Usually squirrels will nest in the spring and summer so wait till fall or winter to do this.
Flying squirrels are much less destructive than grey squirrels.....but still they tend to chew on wires running through the attic, so it is not a good idea to allow them to live there.