How do you treat fungus on a turtle..?

Here's a reliable place to read about skin fungal disease in aquatic turtles:

http://www.austinsturtlepage.com/Care/medshell.htm

Scroll down to "white/brown patches on skin."

I had a Mata Mata with the same fungus you described, his entire nose was eaten away along with large sections of his skin. I went to a very reputable Reptile Vet and he tried everything he knew but it was not successful. My Mata mata died after treatment was ineffective. Mata Mata turtles are some of the hardest species to keep in an enclosed environment...they have to have the water at just the right Ph and the tannins have to be perfect or they will not survive.....

Until the vet gets back to you, try salt.