This study has evaluated self-assembled peptide nanotubes (PNTS) and nanowires (PNWS) as etching mask materials for the rapid and low-cost fabrication of silicon wires using reactive ion etching (RIE). The self-assembled peptide structures were fabricated under mild conditions and positioned on clean silicon wafers, after which these biological nanostructures were exposed to an RIE etching process. Following this treatment, the structure of the remaining nanotubes and nanowires were analyzed by scanning electron microscopy (SEM). Important differences in the behavior of the nanotubes and the nanowires were observed after the RIE process. The nanotubes remained intact while the nanowires were destroyed by the RIE process. The instability of the peptide nanowires during this process was further confirmed with focused ion beam (FIB) milling experiments. The PNTS could stand energetic argon ions for around 32 seconds while the PNWS resisted only 4 seconds before becoming milled. Based on these results, self-assembled PNTS were further used as an etching mask to fabricate silicon wires in a rapid and low-cost manner. The obtained silicon wires were subjected to structural and electrical characterization by SEM and I-V measurements. Additionally, the fabricated silicon structures were functionalized with fluorescent molecules via a biotin-streptavidin interaction in order to probe their potential in the development of biosensing devices.