Bedrock surface topography and thickness of the overlying sediments are key information for numerous engineering applications. However, discrete geological structures, such as bedrock deformation zones, which cause abrupt breaks along bedrock surface, remain largely unrecognized within the conventional digital elevation models (DEMs). This paper provides an example over the generation of geological 3D-models which integrate the deformation zone-controlled erosion surface of the Precambrian crystalline bedrock and the associated thickness variation of the overlying Quaternary glacial sediments in southern Fennoscandian shield. We interpreted the deformation zones from 2D geological and geophysical maps as well as topographic signatures along conventional bedrock surface-DEM, which is based on bedrock surface elevation points comprising >87,000 geotechnical ground investigations, Light Detection and Ranging (LiDAR) and acoustic-seismic datasets. We classified the resulting final deformation zone traces into major, intermediate, and minor classes based on their cross-cutting relationships and lengths, and further used this information in generating an improved, structurally constrained bedrock surface-DEM. As input for the improved bedrock surface-DEM, we assigned the recognized 19 m, 11 m, and 5 m thickness of the load bearing stratum (LBS; basal till, gravel, coarse sand) for the major, intermediate, and minor deformation zones, respectively, and modified the bedrock surface accordingly. The resulting structurally constrained bedrock surface-DEM highlights the pronounced erosion and continuity of the linear topographic depressions occurring along the bedrock surface. The resulting network of linear depressions honors the topology and continuity of the bedrock deformation zones and provides geologically justified depth-to-bedrock constraints also in those areas where very limited geotechnical data is available, and, consequently, the conventional approaches result in excessively high bedrock surface elevations and overly thin overburden. By contrast, areas outside the deformation zones show up to 3 m thick LBS, which indicates that there is no need for bedrock-DEM improvements in those areas. The results can be used for e.g. detailed analysis of seismic hazard associated with the soil amplification, and development of improved bedrock surface modeling methods.