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Si nanowires (NWs) integrated in a field effect transistor device structure are characterized using scanning electron (SEM), atomic force, and scanning Kelvin probe force (KPFM) microscopy. Reactive ion etching (RIE) and vapor-liquid-solid (VLS) growth were used to fabricate NWs between predefined electrodes. Characterization of Si NWs identified defects and/or impurities that affect the surface electronic structure. RIE NWs have defects that both SEM and KPFM analysis associate with a surface contaminant as well as defects that have a voltage dependent response indicating impurity states in the energy bandgap. In the case of VLS NWs, even after aqua regia, Au impurity levels are found to induce impurity states in the bandgap. KPFM data, when normalized to the oxide-capacitance response, also identify a subset of VLS NWs with poor electrical contact due to nanogaps and short circuits when NWs cross that is not observed in AFM images or in current-voltage measurements when NWs are connected in parallel across electrodes. The experiments and analysis presented outline a systematic method for characterizing a broad array of nanoscale systems under device operation conditions.