Methods for fabrication of nanopillar field effect transistors are described. These transistors can have high height-to-width aspect ratios and be CMOS compatible. Silicon nitride may be used as a masking material. These transistors have a variety of applications, for example they can be used for molecular sensing if the nanopillar has a functionalized layer contacted to the gate electrode. The functional layer can bind molecules, causing an electrical signal in the transistor.