Naturally, I don't know any way of treating them that way... Unfortunately, when it comes to fistula... the more "natural" form of treatment seems to be surgery in my opinion. Antibiotics can close some and will often be used in conjunction with another treatment to allow the fistula closure. I don't know what kind of medication you are taking, if any, but generally it's either AZA/6-MP type or, even better suited, the biologics (Anti-TNF: humira, remicade).