A method for determining characteristics of a shim fittable between first and second bodies, comprising: (a) placing optical targets in respective sets of holes in the first and second bodies; (b) scanning respective surfaces of the first and second bodies using a three-dimensional scanner to acquire point cloud scan data, measured hole vector data and other discrete feature data; (c) processing the point cloud scan data, measured hole vector data and other discrete feature data to derive first deviation values representing the deviation of the surface of the first body from a nominal surface of the first body and second deviation values representing the deviation of the surface of the second body from a nominal surface of the second body; (d) correlating the first deviation values with the second deviation values based on a best fit position of the first body relative to the second body; and (e) computing shim gap values based on the correlated first and second deviation values.