Point cloud can provide rich 3-D geometric information of structures, and it has been widely investigated for generating digital functional models, such as finite element (FE) model and building information model (BIM). However, for the existing digital models, how to maintain and update the new local geometric changes on the existing digital models has not been sufficiently studied. Therefore, this research presents a method to update the local 3-D geometric changes on digital functional models using point cloud processing and surface cut. The proposed pipeline starts from processing the point cloud of the local structural change for reconstructing the local surface mesh. After that, the surface mesh is aligned to the corresponding location of the existing digital model by point cloud registration. Then, the geometry updating can be achieved by cutting the digital model with the generated surface mesh. To validate the proposed geometry updating method, two case studies were performed on damaged concrete beams with their intact FE models. The results show that the 3-D geometry changes caused by the damage on the edge and vertex can be successfully updated with high resolution on the existing digital models. The results demonstrate the feasibility of integrating the proposed method into structural health monitoring (SHM) systems for further analysis.