I think the easiest method is to prepare a luring trap for them, either a cave-in variety, or just a simple chamber. Use something destroyable, like a nest box as a lure. Or a longer staying door or floodgate. Might be also an animal if you feel sadistic, but animals don't stay alive long enough. Nest box doesn't stay long too, but FBs can't be stuck with it, unlike doors or floodgates - it happens in tight corridors. I build a serpentine like way, so it takes a moment for them to get there. Then I close the bridge behind, and since bridges are not attacked, that's it. Then either kill it with a cavein trap (easier if it's not a flier, but possible with fliers too) or with marksdwarves, stationed behind a fortification wall (which I also separate with a long, narrow drawbridge working as a curtain, so passing workers won't be scared).
If you feel overwhelmed with tasks, and can't pay much attention to all dangers in the same time, it is possible to make an automatic trap. Since FBs don't trigger pressure plates you must get creative and use something which triggers them (or anything) to close (or open, if that's the setup) the bridge. There are many methods, but two I like is to use an animal on single tile pasture. Is stays there until threatened or killed.
In the first one the animal is pastured over a pressure plate, set to animal weight and triggered by citizens. The plate is connected to a bridge, which can be retracting or raising, no matter, because it is placed upon an access hole from a cavern, with ramp or stairs. When you build the bridge it covers the hole and nothing can pass. When you put an animal on pasture the bridge closes/retracts and opens the path. 100 ticks after removing the animal from the plate the bridge closes the path. Double the linking with a lever, so you may open the bridge while animal is still on the plate, if you want.
In the second, the animal is placed behind a trap, then it is supposed to run through a plate when seeing FB and running for its life (don't use war beasts for this). This is maybe less dependable, so you may want more than one animal, and a bigger pen. When animal passes the plate it triggers that contraption:
http://www.bay12forums.com/smf/index.php?topic=82907.msg2211409#msg2211409 and this one triggers the drawbridge, which in that case works as usual, i.e. it need to be raised to close the path. That way you can make the trap on a single level, without holes. To open the bridge now you can open the door to let the water spread, or just use a level like in the first example.
And have another, external bridge to open - prime - the trap, and keep it closed until needed. You don't want it to be wasted for trolls or crundles.