Lymphocystis is a virus that appears when the fish are stressed. It produces white cauliflower growths over the body. It can spread to other fish but if they are in good conditions and looked after, the virus goes away and will only return if the fish are stressed again. If it is Lymphocystis just leave the fish where they are, and feed them well and do lots of water changes.
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For fungus treatment you can either carefully move them into another tank for treatment, however any further damage to the fish from rough handling, will spread the fungus. So unless the tank is a nice show tank, it is probably better to remove half the filter materials into another tank, then treat the fish in their current tank.
The reason you move half the filter material to another tank is because the Methylene Blue will kill the filter bacteria. By keeping half the filter materials in another tank, you can use that material in the filter after you have finished treating the fish. Then you won't have to worry too much about ammonia and nitrite building up because all the filter bacteria were killed by the medication.