GL, I had to drain my tank to get mine, luckily it was when I moved my tank, and I kept the little guy in the reef. Watch out for the spines, and use a container to get him, nets can hurt them
Sadly I agree with anemonekeeper - there is often no easy way to get a fish out of a stocked reef tank. I normally drain it down about 40% remove rock, it can be a chore.
Removing fish can be tough like stated above. I chased a percula clown for like a week before I got lucky and snagged him. Maybe look into a fish trap.
I recently had to remove an aggresive sailfin from my tank. I started feeding the tank out of a net. Just took the net, put nori in it, and dropped it in, for awhile they were wary, but after a week they had no problem eating out of it. At that point I just waited for the sailfin to come get food and scooped him out. As long as you're gentle with the net, you shouldn't injure him. If you use a big net, you could even scoop him from the net without removing him from the water, with a plastic container.
Fish Trap. Put it in and leave for a few days. Put food in the trap, when they are hungry enough the will go in to get the food. Close the door, if you get multiple fish, release the ones you want back into the tank.
Make a clear box out plexiglas with a hinged door at one end and connect a 1 inch PVC pipe to the top of the other end with a bulkhead. Use fishing line connected to the top of the door and run through a hole in the top of the box near the door to close the door from a distance. Drop food into the PVC pipe from above the water line, grab a cold drink and wait for them to go inside. Has worked for me dozens of times.
I cheated. I had to get rid of a bi-color angel and a maroon clown. I called the LFS and they came and caught them for me. The guy used 3 large nets to entrap them until they swam into one of them. He made it look easy, but I know its not!
I've found getting a 2nd pair of experienced hands work, have the 2nd person in charge of a large net hidden from sight, then lead the fish towards the 2nd person with a smaller net or pointer sticks and scoop them up when they get close and distracted. Has worked several times for me, including an impossible to fish trap catch yellow tang that was too smart to go in the trap for several days, but less than 10 minutes this way.