This article describes a new method for site-specific, atomic force microscope (AFM) fabrication of nanowire heterostructures using electrochemical dip-pen nanolithography (E-DPN). We have demonstrated that E-DPN is ideally suited for the in situ modification of nanoscale electronic devices; the AFM tip and the nanowire device can be used as electrodes and the reactants for the modification can be introduced by coating them onto the AFM tip. Specifically, we have created GaN nanowire heterostructures by a local electrochemical reaction between the nanowire and a tip-applied KOH "ink" to produce gallium nitride/ gallium oxide heterostructures. By controlling the ambient humidity, reaction voltage, and reaction time, good control over the modification geometry is obtained. Furthermore, after selective chemical etching of gallium oxide, unique diameter-modulated nanowire structures can be produced. Finally, we have demonstrated the unique device fabrication capabilities of this technique by performing in situ modification of GaN nanowire devices and characterizing the device electronic transport properties. These results demonstrate that small modifications of nanowire devices can lead to large changes in the nanowire electron transport properties.