We present a MEMS process for the fabrication of arbitrary (adaptable to specific aperture geometries) stabilization of silicon nitride membranes to be used as miniature shadow masks or (nano) stencils. Stabilization was realized by the fabrication of silicon nitride corrugated support structures integrated into large-area thin-film solid-state membranes. These corrugated support structures are aimed to reduce the membrane deformation due to the deposition-induced stress and thus to improve the dimensional control over the surface patterns created by stencil lithography. We have performed physical vapor deposition (PVD) of chromium on unstabilized (standard) stencil membranes and on stabilized (corrugated) stencil membranes to test the proposed stabilization geometry. Both the membrane deformation and the surface structures were analyzed, showing reduced deformation and improved pattern definition for the stabilized stencil membranes. The structures have been modeled using a commercial finite element method (FEM) software tool. The simulation and experimental results confirm that introducing stabilization structures in the membrane can significantly (up to 94%) reduce out-of-plane deformations of the membrane. The results of this study can be applied as a guideline for the design and fabrication of mechanically stable, complex stencil membranes for direct deposition.