This invention provides a system and method for determining correspondence between camera assemblies in a 3D vision system implementation having a plurality of cameras arranged at different orientations with respect to a scene involving microscopic and near microscopic objects under manufacture moved by a manipulator, so as to acquire contemporaneous images of a runtime object and determine the pose of the object for the purpose of guiding manipulator motion. At least one of the camera assemblies includes a non-perspective lens. The searched 2D object features of the acquired non-perspective image, corresponding to trained object features in the non-perspective camera assembly can be combined with the searched 2D object features in images of other camera assemblies, based on their trained object features to generate a set of 3D features and thereby determine a 3D pose of the object.