Abstract Due to the electronic and structural properties of silicon, silicon nanowires have a great potential in nanoscale electronic devices and sensors. Silicon nanowires used for reconfigurable field effect transistors are designed, synthesized and characterized after each step in order to ensure excellent electrical and physical properties of the end product and to study various process parameters. In this study, silicon nanowire based reconfigurable field effect transistors are studied as as-grown “forests”, individually, oxidized and after forming Schottky junctions. The analysis is performed using scanning electron microscopy and transmission electron microscopy. Focused ion beam based preparation was carried out in the case of samples with Schottky junctions. This paper provides a comprehensive description of sample preparation and characterization of the nanowires.