The integration of diverse point cloud sources – such as Terrestrial Laserscanning (TLS), Image Based Modelling (IBM), and Ground Penetrating Radar (GPR) – enables the creation of comprehensive 3D models of archaeological sites, imaging both surface and subsurface structures. Each data type captures distinct information: TLS provides detailed geometry, photogrammetry offers texture and overall structure, and GPR reveals subsurface features. Merging these data sets into a unified point cloud improves the visualisation and facilitates the topographic correction of GPR data, GPR anomaly detection, and digital twin creation, which are essential for archaeological research and cultural heritage preservation. The proposed workflow optimises and georeferences TLS data while ensuring global consistency across multiple scans. Global reference is established by using Global Navigation Satellite System (GNSS) data of distinct features and airborne drone measurements. Comparisons to transform parameters using the geo-located IBM data are conducted and consequently preferred due to visual consistency. The resulting integrated 3D models not only enhance the understanding of the investigated cultural heritage sites but also improve the accuracy of subsurface and surface mapping by correlating overlapping structures from different sensing modalities. This project also demonstrates an automated framework, in which all data are treated as point clouds and merged following precise referencing. A dedicated C++ tool facilitates the optimisation process, and the integration is performed within a Geographic Information System (GIS) framework called Nubigon, suited for the handling of very large data sets. This type of system is pivotal in ensuring that both high-resolution surface details and subsurface anomalies are accurately represented, thereby supporting more effective conservation and research efforts. The custom developed tool is set to be published as open source software, therefore facilitating free access and the possibility of contribution by a broader user base. This encourages transparency and accessibility of software used for the specific purpose of aligning multiple point clouds and optimising the underlying pose graph. GPR data revealed subsurface structures and features within the manor grounds. Anomalies caused by buried walls and foundations of a suspected orangery were discovered beneath the meadow of a terrace adjacent to the building complex. These 3D point cloud data sets and contained structures have been jointely visualized using Nubigon, which overlays IBM surface data with GPR subsurface data to provide a comprehensive representation.