A system and method for estimating dimensions of an approximately cuboidal object from a 3D image of the object acquired by an image sensor of the vision system processor is provided. An identification module, associated with the vision system processor, automatically identifies a 3D region in the 3D image that contains the cuboidal object. A selection module, associated with the vision system processor, automatically selects 3D image data from the 3D image that corresponds to approximate faces or boundaries of the cuboidal object. An analysis module statistically analyzes, and generates statistics for, the selected 3D image data that correspond to approximate cuboidal object faces or boundaries. A refinement module chooses statistics that correspond to improved cuboidal dimensions from among cuboidal object length, width and height. The improved cuboidal dimensions are provided as dimensions for the object. A user interface displays a plurality of interface screens for setup and runtime operation.