A multi-step cleaning procedure cleans phase shift photomasks and other photomasks and Mo-containing surfaces. In one embodiment, vacuum ultraviolet (VUV) light produced by an Xe2 excimer laser converts oxygen to ozone that is used in a first cleaning operation. The VUV/ozone clean may be followed by a wet SC1 chemical clean and the two-step cleaning procedure reduces phase-shift loss and increases transmission. In another embodiment, the first step may use other means to form a molybdenum oxide on the Mo-containing surface. In another embodiment, the multi-step cleaning operation provides a wet chemical clean such as SC1 or SPM or both, followed by a further chemical or physical treatment such as ozone, baking or electrically ionized water.