A semiconductor optical device structure includes passivated facets formed by first removing the native oxide contaminant with a “non-reactive” molecular gas etchant, such as XeF2. As the oxide is removed, a passivation flux is introduced into the vacuum chamber so as to begin the process of forming a passivation layer to cover the exposed facet surface. The gas etchant is slowly turned off and the flux is increased so as to form a passivation layer of the desired thickness on the “cleaned” facet surface. A protective film is then be evaporated to cover the passivation layer.