Twenty years after the last archaeological researches and surveys, a new investigation has been carried out on the basement in the church of Santa Maria in Via Lata in Rome. The study has employed three-dimensional surveys with laser scanning methodology and has focused both on archaeological and architectural issues. Indeed, the present layout of the basement derives from a XVII century remodelling of early Christian and medieval spaces planned by Pietro da Cortona. The architect gave a unique setting and composition to the underground spaces, different in shapes and building materials, thanks to the refinement of his baroque language. Though he worked in small spaces with static problems connected to the foundations and to the loads of the church rising above, and with poor lighting and extreme dampness, Pietro da Cortona put skilfully together “modern” elements with ancient or historical pre-existences. The study focuses on Berrettini’s design process through a three-dimensional analysis with CAD systems, starting from the new XVII century fa?ade and from the articulated distribution of routes that led to the intimate underground interiors. Metrical processing gave the possibility to improve the knowledge about room geometry and to confirm the interpretations put forward by major scholars such as Krautheimer and Cavazzi.