have you tried using a really small car with other clowns in it? that usually gets them.
your corals and nem should be just fine for a little bit without water. obviously the shorter the time, the better, but many of these organisms experience tides in their natural habitat and have at least some ability to cope with being high and dry for short periods of time.
turn off your main tank lights when you drain the water, just to help minimize the stress a little bit.
i've had good success using this fish trap:
http://www.bulkreefsupply.com/index.php/aqua-medic-fish-trap.html
problem with the clowns being they tend not to roam as much. even with my sixline wrasse i caught in it, it took days to convince him to venture in there for food, and only after i didn't feed the tank for 2.5 days.
i think Ray has some great advice there too. i don't know what your rock work looks like, but would it also be possible to use some egg crate or other material to divide the tank off and minimize the area that he's able to swim around? possibly make it easier to net him?
i've also heard of people using mirrors taped to the side of the tank to get their attention and focus their aggression. then when they're going after their reflection, you net them from behind.
good luck!