1. A method of aligning each of a plurality of processing areas regularly aligned on a substrate according to designed alignment coordinates to a predetermined reference position in a static coordinate system for defining a moving position of said substrate, comprising the steps of: measuring coordinate positions, on the static coordinate system, of at least three processing areas selected in advance as specific processing areas from the plurality of processing areas; and determining coordinate positions, on the static coordinate system, of the plurality of processing areas on said substrate by weighting the coordinate positions, on the static coordinate system, of said at least three specific processing areas according to distances between a processing area of interest and each of said at least three specific processing areas in units of processing areas on said substrate, and executing a statistic calculation using the plurality of weighted coordinate positions.