To investigate the geometrical relationships between folding and thrust faulting, we built a 3D geological model of the Helvetic fold-and-thrust belt in eastern Switzerland from several existing and two newly drawn cross-sections in the Säntis area. We partly redrew existing cross-sections and validated them by checking for line length balance; to fill areas with no data we drew additional cross-sections. The model was built based on surface interpolation of the formation interfaces and thrusts between the cross-sections, which allowed generating eight main surfaces. In addition, we used cave data to validate the final model in depth. The main structural elements in the Säntis area, the Säntis Thrust and the Sax-Schwende Fault, are also implemented in the model. The result is a 3D structural model of the area, which provides an intuitive way for examining a portion of a complex structural nappe. The 3D model highlights the shapes of the main anticline-syncline pairs and how these fold trains vary laterally in amplitude and wavelength. It shows how lateral variations in fold style correlate with regional shortening gradients as determined from line-length balancing. The model also clearly shows the lateral extension, the trend, and the variation in displacement along the principal faults. The reconstruction of horizons in 3D allows the investigation of cross-sections in any given direction. The 3D model is useful for developing and understanding how the internal nappe structures, namely folds and thrust faults, change along strike due to palaeogeographic and stratigraphic variations. Lateral stratigraphy variations correlate with different deformation responses of the nappe. Changes can occur either abruptly across transverse faults or in a more gradual manner.