It depends...
Weres are trap avoiders, so when turned into were form they won't be caught by walking over traps. However, once they revert back their powers returns to those of the creatures the are originally, so unless they're kobolds or gremlins, they can be caught in traps by walking over them (I typically catch weres by raising both the drawbridges on my entrance tunnel and lock a door at the inner end to have the wear trying to destroy it. This delays the were sufficiently to make it turn back, at which time I lower the outer drawbridge, so the were will flee, getting caught in the cage traps it passed on the way in).
But: The weres you're after are probably citizens, and citizens do not trigger traps.
However: Citizens can trigger pressure plates if they're set up to do so (the pressure plates, not the citizens), and stunned creatures that end up on cage traps can be caught by the traps (unless they're NOSTUN, which I suspect active weres are). Thus, you can have them cross a pressure plate that cause them to drop when crossing a retractable drawbridge, to fall onto cage traps. If they're citizens you can just order them to do work (such as pulling a lever set to only be usable by those citizens) to get them to go where you want them to go. Just make sure you've got ample time before the next full moon.