This paper introduces a new method for determining the shape similarity of complex three-dimensional (3D) mesh structures based on extracting a vector of important vertices, ordered according to a matrix of their most important geometrical and topological features. The correlation of ordered matrix vectors is combined with perceptual definition of salient regions in order to aid detection, distinguishing, measurement and restoration of real degradation and digitization errors. The case study is the digital 3D structure of the Camino Degli Angeli, in the Urbino’s Ducal Palace, acquired by the structure from motion (SfM) technique. In order to obtain an accurate, featured representation of the matching shape, the strong mesh processing computations are performed over the mesh surface while preserving real shape and geometric structure. In addition to perceptually based feature ranking, the new theoretical approach for ranking the evaluation criteria by employing neural networks (NNs) has been proposed to reduce the probability of deleting shape points, subject to optimization. Numerical analysis and simulations in combination with the developed virtual reality (VR) application serve as an assurance to restoration specialists providing visual and feature-based comparison of damaged parts with correct similar examples. The procedure also distinguishes mesh irregularities resulting from the photogrammetry process.