A system and method for analyzing a surface of an object is provided. The system includes a 3D measurement device operable to acquire a plurality of points on the surface of the object and determine 3D coordinates for each of the points. The system further includes processors operably coupled to the 3D measurement device. The processors are responsive to computer instructions when executed on the processors for performing a method comprising: generating a point cloud from the 3D coordinates of the plurality of points; extracting a first set of points from the plurality of points; defining a first reference geometry through the first set of points; measuring at least one first metric from each of the points in the first set of points to the first reference geometry; and identifying a nonconforming feature based at least in part on the at least one first metric.