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In this study we examine and validate the compatibility of a novel class of discrete peptide nanotubes with standard silicon micro-fabrication processes, in particular with photolithography, thin film deposition and oxide etching processes. We have also studied the alignment of the PNT using micro-fluidic channels. These steps are critical for interfacing nanotubes with external elements, such as metallic electrodes or fluidic channels and may be used as a step towards micro-machined peptide nanotube based devices. Peptide nanotube based devices have a potential in various applications such as nano-fluidics, nano-assembly and bio-sensing applications.