A conductive atomic force microscopy (c-AFM) investigation of GaN nanostructures is reported for strain engineering optoelectronic and piezotronic devices. The use of AFM enables the simultaneous correlation between the surface morphology and charge carrier transport through the nanostructures. The samples under investigation are molecular beam epitaxy (MBE) grown InGaN/GaN nanowires on Ti coated Mo substrate and GaN nanowires on ITO. The metal-semiconductor interface between the metallic substrates and the GaN nanostructures form the bottom contact. A Pt-Ir coated AFM probe is used to create a Schottky top nano-contact. The two interfaces form a metal-semiconductor-metal (MSM) structure. Force and temperature-dependent IV curves are obtained and analyzed, and the MSM structure parameters are extracted. Modulation of both the conductivity and Schottky barrier height (SBH) is revealed. Drastic reduction of the barrier is observed to drive the junctions to ideal MSM under a combination of force and temperature, revealing a dynamic and controlled two-way switching of the devices from rectifying to ideal linear IV properties. Through compressive force modulation by AFM tip, a symmetric 80 meV reduction in SBH at ±0.7 V is realized for the sample grown on Mo. By a combination of temperature and force modulation, a 40 meV increase in SBH is achieved at 0.53 V for the sample on ITO. These results show that the formed structure is ideal for applications in optoelectronics, sensing, piezotronic, piezo-phototronic, and nano-energy harvesting devices.