Balanced restoration consists in removing the effects of tectonic deformation in order to recover the depositional state of sedimentary layers. Restoration thus helps in the understanding of a geodynamic scenario, reduces structural uncertainties by testing the consistency of the structural model, and, under mechanical behavior assumptions, evaluates retro-deformation. We show how an elastic finite element model can be used to solve restoration problems, by setting displacement boundary conditions on the top horizon and contact boundary conditions on the fault cut-offs. This method is generally applied on a tetrahedral mesh, which raises significant meshing problems in complex structural settings, where restoration is particularly useful. Indeed, the mesh has to be conformable to both faults and horizons, including unconformities and onlap surfaces, which may drastically increase the number of elements and decrease the mesh quality. As an alternative, we propose to represent unfaulted horizons as a property of the tetrahedral model, and to transfer the associated boundary conditions onto the neighboring nodes of the mesh, using an “implicit” approach. The proposed methods are demonstrated on a typical example and results show good agreement between both approaches. While the computational time is equivalent in both cases, the time needed for model building is significantly reduced in the implicit case. In addition, the implicit method provides a convenient way to handle unconformities in restoration, both for eroded surfaces, and on onlap layer geometries. In such cases, our method provides a flexible way to specify the amount of eroded material, and generates less mesh elements than the conforming mesh, thereby reducing computational time.