In a method of using and cleaning one or more shadow masks of a shadow mask vapor deposition system used to form an electronic device, a substrate is advanced through series connected deposition vacuum vessels. As the substrate advances through each deposition vacuum vessel, material from a material deposition source positioned in the deposition vacuum vessel is deposited on the substrate through a shadow mask positioned therein. The material is also deposited on a surface of the shadow mask that faces the one material deposition source. Following the deposit of material on the surface of the shadow mask in at least one deposition vacuum vessel, a reactive gas is introduced into the deposition vacuum vessel absent the substrate therein. The reactive gas is then ionized to remove the material deposited on the shadow mask.