Methods, systems, and apparatus including medium-encoded computer program products for generating and visualizing 3D scenes include, in one aspect, a method including: obtaining data regarding (i) standard calibration parts with shapes comprising a cylinder and polyhedrons, and (ii) a limited number of scanning trials performed on the standard calibration parts using a three dimensional (3D) scanner; comparing the data to find shape deviations for the standard calibration parts in a coordinate system; generating a model of functional dependence of scanning error for the 3D scanner using the shape deviations; and providing the model of functional dependence of scanning error for the 3D scanner to quantify scanning inaccuracy of the 3D scanner, wherein the model is usable to predict a measurement error for the 3D scanner on a scanned product.