The aim of this research is to define a method, able to analyse the systems of illumination in the medieval period, through a 3D virtual model reconstruction. It specifically needs to deepen the interactions between natural and artificial illumination in confined spaces. The study describes and examines the best survey technique to obtain a 3D model reconstruction, according to the achievement of such lighting scenarios, and the most suitable tools for lighting analysis. Thus, it is possible to carry out accurate interpretations of the past starting from historical sources and scientific data about lighting. This method was validated on a case study of a rupestrian church in Matera. The rupestrian contexts are less investigated in relation to mediaeval artificial lighting even if there are recognitions and comparative studies of widespread contexts, not only in Puglia and Basilicata, but also in Mediterranean area (e.g. in Cappadocia and Cyprus) which allow identifying evidences related to artificial lighting systems. The architectural signs (hole, niches, etc.) for ancient luminaries can be studied in 3D and lighting prospective. Lastly, the virtual model of the rupestrian church was imported into an opensource visualisation software (3D Heritage Online Presenter) to be appreciable on line and to promote historical heritage knowledge.