In this article, we present issues arising from Terrestrial Laser Scanning of large natural caves using the example of Škocjan Caves, a UNESCO World Heritage Site. Regarding pre-existing tachymetric survey of the passages and volumes calculated from them, the scanning of such a large cave was an even bigger challenge for the team. The cave of almost 6 km long passages with dimensions approx. 30 m x 40 m and max. heights up to 145 m, was scanned from 370 stations. Process of surveying the cave, involves establishing scanner positions through the cave, where scans will overlap, in a progressive route and once back on the surface, collecting, cleaning and stitching the scans into a point cloud 3D model. A total of 8.3 billion points were captured and 2,600 high-resolution photos taken. With Reigl’s RiSCAN Pro software, a point cloud model was registered and then exported to Hexagon’s 3D Reshaper to create a full surface model from which all measurements and calculations were made. Additionally, data acquisition using a camera on an unmanned airborne vehicle was used. By photogrammetric approach, digital terrain model of a surface was built and then tied to the cave model within 3D Reshaper. The resulting high resolution - point cloud model may be used for various purposes such as: volume calculations, detection of geological and speleogenetical features, etc. With a volume of 2.55 million cubic metres, Martel’s Chamber is confirmed to be the 11th largest cave chamber in the world at the moment.