1. A system for generating a representation of flatness defects on a substrate, the system comprising: a memory area for storing an application program; and a processor programmed for: 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 the 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 graphical representation depicting a location of each of the flatness defects on the substrate, wherein generating the graphical representation of the flatness defects includes differentiating in the graphical representation between points having flatness defects disposed between the lower plane and the back side of the substrate and points having flatness defects disposed above the upper plane.