1. A method of generating a representation of flatness defects on a substrate, the method comprising: receiving data describing the thickness of the substrate at a plurality of points on the substrate, the substrate divided into a plurality of sites; defining a reference plane for each of the plurality of sites; defining, for each of the sites, a lower plane spaced from the reference plane towards a back side of the substrate by a threshold value and an upper plane spaced from the reference plane away from the back side of the substrate by the threshold value; determining which of the plurality of points on the substrate represents a flatness defect by identifying which of the plurality of points are not disposed between the upper plane and the lower plane; and generating a representation depicting a location of each of the flatness defects on the substrate.