Geophysical measurement procedures are currently tested in the western Erzgebirge as part of the GeoMetEr project in order to optimize the surface exploration of potential nuclear waste repositories. The research area, which is strictly excluded from the site search, features a deep fault zone in the crystalline basement, the so-called "Roter Kamm". The fault is explored using a combination of seismic, magnetic and electromagnetic methods, and the results are later verified by a 2 km deep research well. Additionally, existing geological and geophysical data, mainly from the historic uranium mining, as well as new data collected during the project will be integrated into a consistent 3D subsurface model. The complex structures in the crystalline rock, which resulted from the multi-phase development of the Erzgebirge, thereby pose considerable challenges. Consequently, the classical modelling procedures, which were rather developed for sedimentary environments, have to be adapted. Here, we present the first results of the structural modelling in the research region. Special attention was given to representing major fault zones, which are assumed to be the primary fluid pathways in the basement. Furthermore, model uncertainties are investigated for selected elements using a self-developed SKUA-GOCAD macro that enables the automatic generation of multiple model realizations.