The application of Au/Si3N4 stencil masks for the transfer of patterns using different MeV-ion beams with various substrates has been investigated. The techniques investigated were namely, conventional lithography with positive- and negative-tone resist polymers, oxygen ion-induced etching of PTFE and patterning using an etch-stop in silicon. We demonstrate that using different well-known microtechnology material-modification techniques, patterns can be transferred using stencil masks and broad ion beams to nanomachining scenarios. In the case of the etch-stop process; writing of 3D micropatterns with different height levels was achieved using a broad beam. The stencil masks were found to be durable with no obvious deterioration and well suited for exposure of large areas.