The fabrication of the lateral polarity-inverted GaN heterostructure on sapphire (0001) using a radio-frequency-plasma-enhanced molecular beam epitaxy is demonstrated. Its microscopic properties such as surface potentials, piezoelectric polarizations, and residual carrier densities were investigated by Kelvin force microscopy and micro-Raman scattering. The inversion from Ga polarity to N polarity in a specific domain and its higher crystal perfection had been unambiguously confirmed by these complementary analyses. The results were also fairly consistent with that of KOH etching, which suggests the applicability of these processes to the fabrication of photonic nanostructures.