Three-dimensional modeling and non-invasive diagnosis are fundamental prerequisites for planning reliable assessments of the seismic vulnerability, renovation and conservation of heritage buildings. In the case of multi-layered, huge and complex ancient constructions, various problems can be encountered in the early design phases of interventions, among which there is often a lack of an adequate building documentation. Such issues include drawings that are without a metric scale, not detailed, not updated or not reflecting the real situation. In addition, the fragility of these constructions requires an accurate census of every sign of deterioration in order to prepare an ad hoc intervention for the site. As an example, in this paper, the results of a survey regarding the Patriarchal Basilica of Santa Maria Assunta (Aquileia, Italy) are reported. The basilica has a rich history of about two thousand years. in which each era has marked the actual architectural layout with its own culture and art. The result is an intricate association of complementary and/or interdependent elements that make the building very complex. Given the need to obtain accurate documentation, a realistic representation and a simulation of the criticalities of the structure, which previously did not exist or were not sufficiently accurate, a multi-methodological and multi-scale diagnosis was performed. In detail, the ground-penetrating radar (GPR) technique was applied to verify the presence of structures still buried under some internal surfaces, and a topographic survey, terrestrial laser scanning (TLS), and structure for motion (SfM) aerial and terrestrial photogrammetry were integrated for the detailed survey of the entire internal and external macro-structure. The resulting outcome provided the comprehensive information needed for preparing projects for the preservation, management and restoration of the basilica and the buildings connected to it.