The use of remote sensing techniques to identify (geo)archaeological features is wide spread. For archaeological prospection and geomorphological mapping, Digital Terrain Models (DTMs) on based LiDAR (Light Detection And Ranging) are mainly used to detect surface and subsurface features. LiDAR is a remote sensing tool that scans the surface with high spatial resolution and allows for the removal of vegetation cover with special data filters. Archaeological publications with LiDAR data in issues have been rising exponentially since the mid-2000s. The methodology of DTM analyses within geoarchaeological contexts is usually based on “bare-earth” LiDAR data, although the terrain is often significantly affected by human activities. However, “bare-earth” LiDAR data analyses are very restricted in the case of historic hydro-engineering such as irrigation systems, mills, or canals because modern roads, railway tracks, buildings, and earth lynchets influence surface water flows and may dissect the terrain. Consequently, a "natural" pre-modern DTM with high depth accuracy is required for palaeohydrological analyses. In this study, we present a GIS-based modelling approach to generate a pre-modern and topographically purged DTM. The case study focuses on the landscape around the Early Medieval Fossa Carolina, a canal constructed by Charlemagne and one of the major medieval engineering projects in Europe. Our aim is to reconstruct the pre-modern relief around the Fossa Carolina for a better understanding and interpretation of the alignment of the Carolingian canal. Our input data are LiDAR-derived DTMs and a comprehensive vector layer of anthropogenic structures that affect the modern relief. We interpolated the residual points with a spline algorithm and smoothed the result with a low pass filter. The purged DTM reflects the pre-modern shape of the landscape. To validate and ground-truth the model, we used the levels of recovered pre-modern soils and surfaces that have been buried by floodplain deposits, colluvial layers, or dam material of the Carolingian canal. We compared pre-modern soil and surface levels with the modelled pre-modern terrain levels and calculated the overall error. The modelled pre-modern surface fits with the levels of the buried soils and surfaces. Furthermore, the pre-modern DTM allows us to model the most favourable course of the canal with minimal earth volume to dig out. This modelled pathway corresponds significantly with the alignment of the Carolingian canal. Our method offers various new opportunities for geoarchaeological terrain analysis, for which an undisturbed high-precision pre-modern surface is crucial.