Turtles produce an incredible amount of ammonia.
The fungal infection you are looking to treat, might be a secondary effect of poor water quality?
What size tank? Filtration? Ammonia, Nitrite?
Pimafix should be fine for turtles, it's all natural and should be safe for them.. I could be very wrong, I would check with the people who produce it.
I would just isolate the turtles in a rubbermaid tote and then treat the tank.. But I can almost guess the turtles messed up your bioload and an ammonia spike caused a fungal infection.
Turtles also can be couriers of many diseases.. The turtles, however, build immunities to these parasites and pathogens and will show no ill effects for the entirety of their life.. while tropical aquarium fish will have zero tolerances to these pathogens.