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The unique electrical properties of silicon nanowires (SiNWs) is one of the reasons it become an attractive transducer for biosensor nowadays. Positive (holes) and negative (electron) charge carriers from SiNWs can simply interact with either positive or negative charge of sensing target. In this paper, we have studied the fabrication of silicon nanowires field effect transistor (SiNWs-FET) nanostructure patterned on 15 Ω resistivity of p-type silicon on insulator (SOI) wafer fabricated via atomic force microscopy lithography technique. To fabricate SiNWs-FET nanostructure, a conductive AFM tip, Cr/Pt cantilever tip, was used then various value of applied voltage, writing speed and relative humidity were studied. Subsequent, followed by wet etching processes, admixture of tetramethylammonium hydroxide (TMAH) and isopropyl alcohol (IPA) were used to remove the undesired of silicon layer and diluted hydrofluoric acid (HF) was used to remove the oxide layer. From the results, it shows that, cantilever tip at 9 V with 0.4 μm/s writing speed and relative humidity between 55% - 60% gives the best formation of silicon oxide to fabricate SiNWs-FET nanostructure.