The task of documentation and conservation of Cultural Heritage defines the challenges that geomatics techniques have to overtake in order to provide different solutions that combine the automation of processes with accurate results. The employment of integrated technologies allows improving the documentation of Cultural Heritage from a quantitative and qualitative point of view. The use of range and image-based techniques ensures the possibility to completely record articulated structures such as building with underground environments. The latter present often problematic survey conditions that imposed well planned and appropriate solutions. In this context, the paper presents the results of a 3D survey of the underground “Sybil hypogeum” and the related overhead church located in the Archaeological Park of Lilibeo (Marsala, Southern Italy). An integrated survey was planned in order to combine laser scanning technology with terrestrial-based and Unmanned Aerial Vehicle (UAV)-based photogrammetry to acquire the three-dimensional data of the whole complex (underground environments and overhead church). The aims of the work are related to test a topographic approach by a traverse method for scans registration and to archive a complete and detailed 3D model of the whole area. This model could be used to prevent the risk of information’s loss and to improve the knowledge of the site.