There are two ways of destroying the pesky enclave vertibirds that drop soldiers and robots in various locations throughout the nuked DC area.

These methods are:

• When you are near a vertibird equip the "Fat Man" nuke launcher. Obviously, you nuke them. One shot, one kill. My favorite past time is to hunt them down and blast them out of the radioactive sky after they drop the troops. Unfortunately I only had about 16 nukes and I only found a few vertibirds, but I’m still hunting.
• When the vertibird is in sight you can use the missile launcher. It takes about 3 missiles to destroy one vertibird. This is easyer to accomplish when you have many action points (AP). Typically you only get to hit them about three times. So, good luck.

I wish I could have flown one.