We studied the interaction of active molybdenum field emitter arrays with molecular hydrogen and helium. Upon impact with the field emitted electrons, H-2 gas introduced into the system undergoes dissociation and ionization. The emitter surface is conditioned through the interaction of the hydrogen atoms and ions with molybdenum, resulting in the formation of volatile molybdenum hydrides. The volatile species are removed by the vacuum system. Surface conditioning of the tips is reflected in the reduced work function and increased electron emission. Emission enhancement reaches a maximum for total exposures of 1000-1500 L (1 L = 1x10(-6) Torr s) of H-2. For small exposures of helium (<1500 L), emission enhancement is also observed. Larger exposures result in significant emission degradation, We propose that the interaction of H-2 With active molybdenum field emission arrays can be used as an efficient, ultrahigh vacuum compatible method for in situ cleaning of the field emitter arrays.