Incorporating prior geological knowledge in geophysical process models often meets practical meshing challenges and raises the question of how much detail is to be included in the geometric model. We introduce a strategy to automatically repair and simplify geological maps, geological cross-sections and the associated meshes while preserving elementary consistency rules. To identify features breaking validity and/or the thin features potentially problematic when generating a mesh, we associate an exclusion zone with each model feature (horizon, fault). When these zones overlap, both the connectivity and the geometry of the geological layers are automatically modified. The output model enforces specific practical quality criteria on the model topology and geometry that facilitates the generation of a mesh with lower bounds on minimum angles and minimum local entity sizes. Our strategy is demonstrated on an invalid geological cross-section from a real-case study in the Lorraine coal basin. We further explore the impacts of the model modifications on wave propagation simulation. We show that the differences on the seismograms due to model simplifications are relatively small if the magnitude of simplifications is adapted to the physical problem parameters.