Copper is not a viable option either.
Medicating a reef tank is always a very bad idea, especially if using something lethal as copper. It will contaminate the rocks and sand and render all useless for a reef tank (plus you will have a hard time to maintain therapeutic copper levels - it is an outright stupid idea.
What fish do you have in there and how large is your tank?
What "plants" do you have in this tank?
What disease are you treating?
In general you can always catch all fish either by:
!. using a trap with either food or a mirror as "bait"
2. using a hook
3. letting nearly all the water out of the tank and pick them off
4. collecting them in their sleeping places at night
... check the sticky
Catching an uncatchable fish for more options and ideas.
There is always a method (or a combination of several) to catch all fish out of a tank.
But if you are not able to catch all the fish and you don't want to break down/empty the tank to get all the fish out you have only one option left: just let the fish ride it out and see who survives.