Three-dimensional virtual modeling is one of the tools being rapidly implemented in the construction industry, leading to the need for strategies based on intelligent 3D models of cities and/or digital twins, which allow simulation by interacting with their real physical counterparts, anticipating the outcomes of decision making. In practice, problems arise when creating and managing these twins, as different data, models, technology, and tools must be used, and they cannot all be combined as desired due to certain incompatibilities. On the other hand, today’s traditional building management demands a more optimized process to prevent errors and enable timely reactions to failures and defects. Managing and using a large amount of complex and disparate data are required, which is why the use of CMMS-type software is common (Computerized Maintenance Management System). However, such software is rarely designed for management in a 3D format, often due to the absence of three-dimensional models of the assets. This research aims to contribute to the technological development of the digitalization of the built environment, providing a simple methodology for generating and managing 3D models of cities. To achieve this, the tools and information useful for generating an integrated GIS 3D and BIM model, and for Computer-Aided Maintenance Management in a three-dimensional format (CMMS-3D), are identified. The final model obtained is used to optimize the three-dimensional management of a classroom building on the “Campus de Las Llamas” at the University of Cantabria in Spain. The results demonstrate that it is possible to integrate digital models with simple linking mechanisms between the existing tools, thus achieving an optimal three-dimensional management model.