Abstract: Described herein are photomask blanks and photomasks prepared therefrom, methods for producing the photomask blanks and apparatus used in such methods. In one aspect, there is described methods for preparing photomask blanks having layers with a compositional gradient, i.e., a varying composition through the thickness of the layer. In other aspects, either in conjunction with the above aspects or independently, methods and apparatus are provided which allow more efficient use of a cluster tool for preparing the photomask blanks and performing quality control on them. The inventions find applicability, for example, in preparing binary photomask blanks and phase shift photomask blanks.