Hydrogen in hydrofluorocarbon plasmas plays an important role in silicon nitride (Si3N4) reactive ion etching. This study focuses on the elementary reactions of energetic CHF2+ and CH2F+ ions with Si3N4 surfaces. In the experiments, Si3N4 surfaces were irradiated by monoenergetic (500–1500 eV) beams of CHF2+ and CH2F+ ions as well as hydrogen-free CF2+ and CF+ ions generated by a mass-selected ion beam system and their etching yields and surface properties were examined. It has been found that, when etching takes place, the etching rates of Si3N4 by hydrofluorocarbon ions, i.e., CHF2+ and CH2F+, are higher than those by the corresponding fluorocarbon ions, i.e., CF2+ and CF+, respectively. When carbon film deposition takes place, it has been found that hydrogen of incident hydrofluorocarbon ions tends to scavenge fluorine of the deposited film, reducing its fluorine content.