The top-down fabrication of high aspect ratio circular micro-and nanostructures in silicon nitride is presented. A new method is introduced to increase the aspect ratio of anisotropically etched holes by a factor of more than two with respect to the results obtained from an established dry-etching process. The method is based on the renewal of an etching mask after a first etching step has been completed. Mask renewal is done by line-of-sight deposition of a masking layer on the surface of the sample, which is mounted at an angle with respect to the deposition direction. No additional alignment step is required. The proof of principle is performed for silicon nitride etching through a mask of titanium, but the method has great potential to be applicable to a wide variety of substrate-mask combinations and to find entrance into various engineering fields. Two specific applications are highlighted. Firstly, a thick silicon nitride hardmask is used for the fabrication of deeply etched photonic crystal holes in indium phosphide (InP). For holes of 280 nm diameter, a record aspect ratio of 20 and an overall selectivity of 28.5 between a positive-tone resist layer and InP are reported. Secondly, the use of perforated silicon nitride membranes for droplet formation for applications in food engineering or pharmaceutics is addressed. Preliminary results show a potential for the self-aligned mask renewal method to exceed state-of-the-art membrane quality in terms of pore size, aspect ratio and membrane stability.