This essay describes the combination of 3D solutions and software techniques with traditional studies and researches in order to achieve an integrated digital documentation between performed surveys, collected data, and historical research. The approach of this study is based on the comparison of survey data with historical research, and interpretations deduced from a data cross-check between the two mentioned sources. The case study is the Basilica of S. Ambrogio in Milan, one of the greatest monuments in the city, a pillar of the Christianity and of the History of Architecture. It is characterized by a complex stratification of phases of restoration and transformation. Rediscovering the great richness of the traditional architectural notebook, which collected surveys and data, this research aims to realize a virtual notebook, based on a 3D model that supports the dissemination of the collected information. It can potentially be understandable and accessible by anyone through the development of a mobile app. The 3D model was used to explore the different historical phases, starting from the recent layers to the oldest ones, through a virtual subtraction process, following the methods of Archaeology of Architecture. Its components can be imported into parametric software and recognized both in their morphological and typological aspects. It is based on the concept of LoD and ReverseLoD in order to fit the accuracy required by each step of the research.