There are two possible causes of finrot...

1) A water mould known as Saprolegnia.

2) A secondary-infection from internal bacteria known as Columnaris.

In the latter case you will need to treat for an internal-bacterial infection, API pimafix is one of the best medications on the market. Separating the affected fish is the best thing to do however you still need to treat the main aquarium.

Stripping down the aquarium is unlikely to help as eventually it will build up small background populations of harmful bacteria and parasites, these aren't usually a problem however they will cause problems when the fishes immune systems are compromised due to stress. A major cause of stress is poor water quality, so I would test the water for pH, ammonia, nitrite and nitrate. Also post the test results if you can.

Finally a photo of the affected fish would be useful.