In this study the surfaces and cross sections of deteriorated Coptic mural paintings were investigated using Computer Tomography (CT) scan images and video, and points (voids) on the surface were analyzed. To our knowledge, it is the first report on the application of CT scan for the investigation of deteriorated Coptic mural painting surfaces in Upper Egypt. The samples tested were collected from two sites: the Monastery of Martyrs (Deir alShuhada-Esna) and the Luxor temple. The selection of these monasteries was due to their historical importance, which is directly related to Egyptian Coptic heritage. The deteriorated surfaces of the selected mural paintings were characterized using new avenues of computed X-ray tomography (CT scan) in order to gather sufficient information about their composition and structure. The obtained results show that CT scan images provided us with detailed information about the sample porosity and structure. In the case of the Martyrs monastery, it was found that the mural paintings consist of one layer which contains clay minerals (kaolinite, montmorillonite, and illite) in the form of coarse plaster. On the other hand, the Martyrs Monastery showed higher porosity than the Roman Fresco in the Luxor Temple.