The research aims to present an innovative methodology to execute the Heritage conservation processes in a collaborative and interdisciplinary BIM project, with an effective management of the deterioration suffered over time, emphasizing the structures and coatings. The research begins with the architectural survey using scanning techniques (TLS) and terrestrial photogrammetry (SfM) and taking as a study the Duomo of Molfetta (Italy), a unique Romanesque architecture of Puglia (Italy). The methodological process is mainly aided by the precise semantic segmentation of global point clouds, a semi-automatic process assisted by classification algorithms implemented in the post-processing software, and which has allowed the classification of the unstructured information provided by the remote sensing equipment when identifying the architectural-structural systems of a building with high historical values. Subsequently, it has been possible to develop an efficient Scan-to-HBIM workflow, where the Heritage-BIM (HBIM) project has fulfilled the function of a database by incorporating and organizing all the information (graphic and non-graphic) to optimize the tasks of auscultation, identification, classification, quantification and, in turn, facilitating the parametric modeling of unique structures and architectural elements. The results have shown great effectiveness in the processes of characterization of architectural and artistic heritage, focusing on the deformations and deterioration of the masonry in columns, and making multidisciplinary conservation work in an HBIM project more flexible. But there are still some difficulties for the automatic interpretation of 3D point cloud data, related to specific systems of the historical architecture. In conclusion, human action and interpretation continues to be a fundamental pillar to achieve precise results in a heritage environment.