In 2007, the remains of an extended Roman villa rustica, only partially known from old excavations, were detected through high-resolution GPR measurements at Oberlienz-Lesendorf (Austria). The archaeological prospection was conducted by the Vienna Institute for Archaeological Science (VIAS) in collaboration with the Department of Archaeologies of Innsbruck University and ZAMG Archeo Prospections. Despite the important discovery, the Roman villa in Oberlienz-Lesendorf was not further investigated in the years that followed the GPR survey. In this article the main steps of the GPR survey are described. Attention is focused on the GIS-based archaeological interpretation of the data through the 3D approach. An optimised workflow, based on the efficient integration of ArcGIS with 3D modelling software (3D Studio Max and MeshLab), has been developed. The process, which included the necessary comparisons with a few Roman villas in Austria and Germany (Bavaria), resulted in a semi-reconstructive 3D digital model of the Roman villa. The work, focused on methodological aspects, was conducted by the first author in close and interdisciplinary collaboration with the team of the Ludwig Boltzmann Institute for Archaeological Prospection and Virtual Archaeology (LBI ArchPro) as part of her dissertation at the University of Vienna, which was concluded in 2017.