1. A method of aligning a patterned substrate having a plurality of segments and measuring the same, the method comprising: defining a point of interest for each segment of the patterned substrate; locating a first point of interest in a first segment of the patterned substrate, the first point of interest being within a single die of a semiconductor wafer; scanning a first area of the patterned substrate proximate the first point of interest for a first unique feature within the single die; saving a scanned image of the first area; defining a periodicity for the patterned substrate, the periodicity corresponding to the scan area of a raster movement used in locating the first unique feature; locating a second point of interest in a second segment of the patterned substrate; scanning a second area of the patterned substrate proximate the second point of interest, based on the defined periodicity used in locating the first unique feature, for a second unique feature corresponding to the first unique feature, wherein the first unique feature is saved as an alignment image for use in locating the second unique feature in the second area; mapping the alignment of the substrate with respect to tooling in which it is disposed with; measuring the second point of interest; and locating a third point of interest in a third segment based on the periodicity.