Total break down, start with new rock .
That's drastic! There must be something that can be done other than this. If this was my only option, I would not re-start. I would just leave it down. Too much work and expense to start over.
How can I eradicate brown Polyps?
My 90 gal reef is being overtaken.
So a picture would REALLY help, are you talking about brown button polyp? or are you talking like Aiptasia which kinda looks like a brown polyps? so pictures would help but, that being said there is ALWAYS a way to kill corals. if its just a couple polyps and different rocks you can inject the polyps with highly concentrated salt water with a syringe (a 90 gallon should have enough water to dilute the salt you inject in). if its aiptasia you can throw a copperband in the tank to take care of it (as long as you are willing take extra care of feeding it after the aiptasia is gone.)! also when the copperband gets older he could very well outgrow a 90 gallon. sorry it was so long winded but hope it helps!
best advice for the op is to carefully remove the rock and go trade it in at your lfs for some store credit and replace it with new rock.
you want to be excruciatingly careful when dealing with zoa's and paly's, especially paly's.
they are very likely to contain palytoxin, so any kind of efforts aimed at killing them will also likely end up releasing palytoxin as the palys die. this has some obvious and very real dangers.
i've read about people getting very sick by using boiling water injection which can aerosolize the palytoxin and cause all kinds of nasty issues.
likewise with other methods that kill them in tank people have gotten severe dermatitis reactions or other extremely negative side effects after having hands in the tank then touching something else like their eye, or having a pet come by and lap up some of the water.
paly's are not to be messed with. that's why i don't keep them.
best advice for the OP is to carefully remove the rock and go trade it in at your LFS for some store credit and replace it with new rock.
nuking these things can be very dangerous.
Well ...thats what I was saying..:wavehand:
The more you guys talk about corals, the more I'm thinking of going fish only.
The whole Palytoxin scare has been blown way out of proportion IMO. You probably put yourself at more risk by DRIVING to the LFS to buy these corals than you do by handling them. (or any coral for that matter)
Btw those polyps can be eradicated with a sharp pair of scissors, some epoxy and a lot of patience.