uv, you're so nice.
It is possible to remove the filter and just do water changes on display. I often dont recommend this to new people because they dont yet understand all the complex issues that it takes to make this work. Alot can go wrong. But, this is an option. However, daily water changes are absolutely necessary to keep organic load low. The higher the organic load, the less effective the uptake of the medication (organics offset antibiotic effectiveness). But, also, obviously, taking some biological bacteria away from system, increases the chance of ammonia or /and nitrite spike. A sick fish is even more vulnerable to this occuring at lower levels.
The kanamycin, neomyacin, and nitrofurazone ( can kill or set-back certain plants temporarily) are safe for bio-filter. Erythromycin- no.
It is always best to treat in hospital tank when you can. My hospital tanks are not pre-cycled because I want them sterile. I set it up as needed. Through daily water changes I ensure optimum uptake of meds and no chance of ammonia/nitrite toxicity.
Just saw this. Will have to think on this while waiting for the kanamycin to form my gameplan. Will definitely do a most thorough maintenance including filters and gravel vac to reduce organics amap. Coincidentally, just checked my Cerges reactor and hoses and realized they have been going for a year without cleaning so add those to the list. Outstanding advice as always.
So sorry to see your sick fish. I would second everything DiscusLuv said. If it were my tank and my fish, and I wanted to treat the whole tank, I would take the filters off (leave a powerhead or something for circulation). If you don't have anything else to keep the circulation going remove the filter media and put that in your hospital/quarantine tank (needs to stay wet and circulated to keep BB alive). With the filters off you will need to do daily water changes.
After removing the filter media I would treat with recommended doses. You can usually find API meds at petsmart for fast availability. If using API, I would use fungus cure + erythromycin or Furan-2. If you leave your filter in it will kill it as Discusluv said. These meds are pretty powerful reducing agents especially when used together so it isn't a bad idea to add another airpump/airstone when you treat. The extra air will help your fish.
Honestly the best option is to remove all the affected fish into a hospital tank (or bucket) so that you don't ruin your display tank and have to start over. Good luck, and I'm subscribed to watch for updates.
EDIT: If you decide to treat the whole tank and take off your filter DON'T FEED YOUR FISH. No need to produce the extra ammonia and they will be fine without.