If a modification artist is said to be underground, it generally means that they are working without recognition from their "governing community."
An underground cutter is a surgical practitioner working without the approval of the medical community. A slight variation on that would be the underground doctor who is recognized by the medical community, but also does work "underground"—typically this includes doctors willing to quietly perform subincisions, castrations, amputations, and so on, with relatively few questions asked. Often, these procedures take place outside of their mainstream studio (ie. in a hotel room, or a medical fetish club), or often in a studio in a country like Mexico with less restrictions on doctors' actions.