The nanotechnology world is being more and more attracted toward high aspect ratio one-dimensional nanostructures due to their potentials as building blocks for electronic/optical devices. Here, we propose a novel method to generate nanowire patterns with assistance of superhydrophobic flexible polydimethylsiloxane (PDMS) substrates. Micropillar gaps are tunable via a stretching process of the PDMS surface; thus, diverse nanowire patterns can be formed by stretching the same PDMS surface in various ways. Importantly, square nanowire loops with alternative compositions can be generated through a double-stretching process, showing an advanced methodology in controlling the alignment of nanowires. Since alternative fluorescent molecules will be quenched by diverse chemical substances, this alternative nanowire loop shows a selective detection for diverse target compounds, which greatly improves the application of this nanowire patterning approach. Furthermore, such alternative nanowire patterns can be transferred from pillar-structured surfaces to flat films, indicating further potentials in microcircuits, sensitive sensors, and other organic functional nanodevices.