Damage mapping is considered a critical stage in the correct diagnosis of the state of conservation of Cultural Heritage manifestations. The common approach generally implies a large user interaction to map the different pathological processes presented on 2D documents such as elevations or sections, among others. In contrast with this practice, the present paper proposes a semiautomatic 3D-methodology, with a minimum user interaction, able to accurately analyse both radiometric and geometric data recovered by a non-contact technology (Terrestrial Laser Scanning), allowing the extraction and quantification of a wide diversity of pathological processes from biological colonization to deformations. This approach is therefore a potential tool for the rapid and accurate diagnosis of Cultural Heritage. To confirm the applicability and potential offered by the proposed methodology, a highly affected historical masonry, the San Francisco Master Gate of the Almeida Fortress (Portugal), was evaluated by using the Faro Focus 3D 120 Laser Scanner.