Methods are disclosed for generating a representation of flatness defects on a wafer. Data is received describing the thickness of the wafer at a plurality of points on a wafer divided into a plurality of sites. A reference plane is defined for each of the plurality of sites. For each of the sites, an upper plane and a lower plane are defined relative to the reference plane. A determination is made as to which of the plurality of points on the wafer represents a flatness defect by identifying which points are not disposed between the upper plane and lower plane. A representation is then generated depicting a location of each of the flatness defects on the wafer. In some embodiments, a single representation is generated depicting the location of flatness defects on a plurality of wafers.