In this article we demonstrate the use of self-assembled peptide nanotube structures as masking material in a rapid, mild and low cost fabrication of polymerized p-toluenesulfonate doped poly(3,4-ethylenedioxythiophene) (PEDOT:TsO) nanowire device. In this new fabrication approach the PEDOT:TsO nanowire avoids all contact with any organic solvents otherwise traditionally used in clean room fabrication. This can be achieved due to the intriguing properties of the self-assembled peptide nanotubes utilized as a dry etching mask for the patterning of the PEDOT:TsO nanowire. The peptide nanotubes, despite remaining stable during the reactive ion etching procedure, can be dissolved rapidly in water afterwards. The fabricated PEDOT:TsO nanowire devices exhibit excellent electrical characteristics. Finally, the potential of PEDOT:TsO nanowires as temperature sensors has been demonstrated and the high resolution of the sensor was illustrated.