A system and method for selecting among 3D alignment algorithms in a 3D vision system is provided. The system and method includes a 3D camera assembly to acquire at least a runtime image defined by a 3D point cloud or runtime 3D range image having features of a runtime object and a vision system processor. A training image is provided. It is defined by a 3D point cloud or 3D range image having features of a model. A selection process is operated by the vision processor. It analyzes at least one training region of the training image having the features of the model and determines a distribution of surface normals in the at least one training region. It also selects, based upon a characteristic of the distribution, at least one 3D alignment algorithm from a plurality of available 3D alignment algorithms to align the features of the model with respect to the features of the runtime object.