1. A model-based measurement method, comprising: searching a mask design database to identify a measurement site for a photomask, wherein the measurement site contains a pattern identified to be suitable for pattern registration measurement; obtaining at least one optical image of the measurement site specified for the photomask utilizing an imaging device; retrieving a design of photomask from the mask design database; selecting a portion of the design corresponding to the specified measurement site; generating at least one simulated image of the selected portion of the design based on a computing device implemented model of the imaging device; adjusting at least one parameter of the computing device implemented model to minimize dissimilarity between said at least one simulated image and said at least one optical image, wherein said at least one parameter includes at least one pattern registration parameter indicative of a shift of the pattern on the photomask; and reporting said at least one pattern registration parameter of the computing device implemented model when the dissimilarity between said at least one simulated image and said at least one optical image is minimized.