Structure-from-motion photogrammetric processing and laser scanning technology have given us more tools to study environments such as caves with their complex and unique morphology. In this case study, we combine two innovative techniques to generate the complete 3D model of a show cave (Koutouki, Peania Greece) and calculate the rock thickness between the cave and the open surface. We used a Handheld Laser Scanner (HLS) for acquiring points with coordinate information covering the entire cave and an Unmanned Aerial System (UAS) for acquiring data covering the open-air surface above the cave. The absolute and exact placement of the point cloud within a geographic reference frame allow the three-dimensional measurements and detailed visualization of the subsurface structures. By processing of the multi-source data (UAS and HLS) we managed to make a quantitative analysis of the terrain. After a series of processing steps and analyses we managed to calculate with high accuracy several dimension such as the cavity vacuum, the speleothem volume, the elevation differences across the entire cave etc. The final product is a high-resolution information layer with measurements of the rock thickness between the roof of the underground karstic landform and the open-surface topography.