Are there biocompatible materials available to the general public?
There are printers designed for medical use, and the manufacturers supply them with varying levels of certification and testing, however I've not seen a filament manufacturer certify their material as bio-compatible separate from the printer. The printing process changes the material slightly in the best case (and significantly with poor temperature control or badly set parameters), so even if bio-compatible filament were found, the resulting product might not achieve the same level of bio-compatibility.

If your intent is to use hobbyist level machine for medical purposes, you might simply want to use an interface, such as a sock or a molded/cast polymer that you know to be bio-compatible between the printed part and the skin.