High resolution archaeological geophysical prospections allow for the non-invasive investigation of subsurface features. In particular, the high resolution Ground Penetrating Radar (GPR) measurements permit the accurate 3D investigation of the subsoil offering the possibility for the detailed 3D mapping of archaeological structures and virtual reconstructions of the archaeological complexes. In this paper we present a 3D reconstruction of a Roman Villa located in Oberlienz-Lesendorf (Tirol, Austria), part of the former Roman province of Noricum, which has been investigated by GPR. The 3D GIS-based mapping of the features detected by GPR is conducted within ArcGIS 10.2 allowing for the improved 3D editing of vector features and detailed description through attributable information. Extruded 2D (2.5D) and 3D interpretation models of the buried Roman structures are created based on the dynamic and interactive analysis of the prospection data in the GIS environment, in which the GPR data are visualized in form of animated sequence of raster images. Based on the GIS interpretation models the virtual reconstruction is performed within 3D modelling software environment allowing for the interactive modelling and texturing of the mapped 3D objects. In this step, analogies together with written sources play a crucial role since they provide additional data and documentation which can be used to enrich the lack of information. A systematic comparison between the detected remains and excavated archaeological sites in the provinces Noricum and Raetia, where similar buildings and complexes have been investigated, was conducted with the goal to achieve a comprehensive and reliable reconstruction of the Roman villa. In order to achieve the interactive investigation of the virtual 3D model in a georeferenced environment, the textured 3D objects are re-imported into the 3D ArcGIS environment (ArcScene and ArcGlobe) and integrated into the GIS-based 3D maps, in which the objects and related attributable information can be queried, interactively, by means of HTML popups. Structures belonging to different phases are clearly detectable in the GPR data. Finds dating to different periods were also collected at the site at the beginning of 20th Century. Based on this fact, we argued that the Roman villa was probably used for a period of at least 300 years. Based on the analysis of the GPR data and analogies with similar complexes, the presumed diachronical evolution of the Roman villa with main houses and ancillary buildings is presented dynamically through the use of animations. The work which was conducted within the multidisciplinary team of the Ludwig Boltzmann Institute for Archaeological Prospection and Virtual Archaeology in collaboration with the Vienna Institute of Archaeological Science (VIAS) of the University of Vienna, also has the aim to demonstrate the high potential of the integrated and systematic use of non-invasive Archaeological Prospection Methods and Virtual Archaeology for the investigation, digital documentation and scientific dissemination of the ``invisible'' archaeological heritage. Keywords: GPR archaeological prospection, 3D GIS, 3D modelling, Roman Villa, Virtual Archaeology.