Need to align structural models? This paper presents a method for automated best-matching alignment of three-dimensional models represented by ensembles of points. The method can be used for comparative analysis of structural models obtained by different methods, e.g., of high-resolution crystallographic atomic structures and low-resolution models from solution scattering or electron microscopy. A normalized spatial discrepancy (NSD) is introduced as a proximity measure between three-dimensional objects, minimized by the algorithm after inertia-axes alignment. The final value of the NSD provides a quantitative estimate of similarity between the objects. A computer program implements the introduced spatial discrepancy proximity measure. Simulations have been performed to test its performance on model structures with specified numbers of points ranging from a few to a few thousand. The method's utility lies in its ability to quantitatively assess similarity between structural models derived from various techniques. The method can be used for comparative analysis of structural models obtained by different methods. The method can be used for comparative analysis of structural models obtained by different methods. This has applications for structural comparison.