Plural shot areas arranged in succession in a two-dimensional array on a substrate are aligned to a predetermined reference position in a fixed coordinate system. At least three of the plural shot areas are selected as specified shot areas. Coordinate values (positions) of alignment marks associated, respectively, with the specified shot areas are measured. Anticipated coordinate values are calculated from preset coordinate values, based on an array model of the shot areas, predetermined by a first equation. A unique relation defined by a second equation is assumed, between the anticipated coordinate values and actual coordinate values in the alignment. Parameters of the relation are determined so as to minimize the average error between the measured coordinate values and coordinate values calculated from the relation. Actual coordinate values of the shot areas on the substrate are calculated based on the parameters and the anticipated coordinate values.