The chapter presents a reflection on the concept of transparency in digital modeling and visualization of Architectural Heritage. Moving from topics of transparency and from the experiences in using paradata in different fields to state model's source, the degree of reliability of virtual re-constructions, and to made the digital model testable by other professionals, transparency and paradata are studied and declined for a dedicated application to historical buildings. In fact paradata is useful for model's design, use, management, diffusion, archiving, and interoperability. This according to an aim of model's intellectual transparency, and scientific computing and visualization of historic buildings. Follows issues about: the relationship between physical and digital heritage, the design of the digital 3D model and the database, the communication of transparency through spatial visualizations and multiple windowed representations, the transparency as possible methodological workflow for scientific analysis.