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The reliable and reproducible fabrication of nanostructures by stencil lithography (SL) faces three main challenges: the stability of the thin stencil membranes with nanoapertures, the blurring of the deposited structures, and the clogging of the nanoapertures in the stencil membranes. This study reports on these three important issues and presents corresponding solutions for the patterning of nanostructures by SL. To increase the stiffness and the stability of the membranes, we have used a hexagonal array of corrugations to globally reinforce the stencil membranes. To correct the blurring, we have used a corrective etching that improves the definition of Al nanostructures. Using this corrective etching, we have fabricated poly-Si nanowires. Finally, we have used metal wet etching to remove the material accumulated on the membranes as a remedy to the clogging.