We applied spatially shaped ultra-short pulses for laser micro-machining on the SiNx/c-Si layer system for the investigation of the selectivity ablation behavior of the sub-micrometer-thick SiNx top layer. In comparison to Gaussian beams, intensity spatially shaped pulses have the potential to minimize the superfluous energy in the peak region over the ablation threshold fluence as well as a steeper intensity drop at the side edge of the pulses. This can lead to more precise lateral and vertical ablation properties of the top thin film layer and lower modification or damage to the silicon substrate and the adjacent region. We compare the ablation variations due to beam shaping via light microscopic measurements on the micrometer-laser spot structures as well as the crystalline phases and stress modification via μm-Raman in the ablated spot, adjacent modified regions, and untreated reference areas. We focus on the design and fabrication of silicon membranes as advanced filters with a particular emphasis on controlling pore size and inter-pore distances to optimize filtration performance.