Abstract Periodic arrays of deep nanopores etched in silicon by deep reactive ion etching are desirable structures for photonic crystals and other nanostructures for silicon nanophotonics. Previous studies focused on realizing as deep as possible nanopores with as high as possible aspect ratios. The resulting nanopores suffered from structural imperfections of the nanopores, such as mask undercut, uneven and large scallops, depth dependent pore radii and tapering. Therefore, our present focus is to realize nanopores that have as cylindrical as possible shapes, in order to obtain a better comparison of nanophotonic observations with theory and simulations. To this end in our 2-step Bosch process we have improved the mask undercut, the uneven scallops, pore widening and positive tapering by optimizing a plethora of parameters such as the etch step time, capacitively coupled plasma (ion energy) and pressure. To add further degrees of control, we implemented a 3-step DREM (deposit, remove, etch, multistep) process. Optimization of the etching process results in cylindrical nanopores with a diameter in the range between 280 and 500 nm and a depth around 7 μm, corresponding to high depth-to-diameter aspect ratios between 14 and 25, that are very well suited for the realization of silicon nanophotonic structures.