The non-centrosymmetricity of III-nitride wurtzite crystals enables metal or nitrogen polarity with dramatically different surface energies and optical properties. In this work, III-polar and N-polar nanostructured ultraviolet multiple quantum wells (UV-MQWs) were fabricated by nanosphere lithography and reactive ion etching. The influence of KOH etching and rapid thermal annealing treatments on the luminescence behaviors were carefully investigated, showing a maximum enhancement factor of 2.4 in emission intensity for III-polar nanopillars, but no significant improvement for N-polar nanopillars. The discrepancy in optical behaviors between III- and N-polar nanopillar MQWs stems from carrier localization in III-polar surface, as indium compositional inhomogeneity is discovered by cathodoluminescence mapping, and a defect-insensitive emission property is observed. Therefore, non-radiative recombination centers such as threading dislocations or point defects are unlikely to influence the optical property even after post-fabrication surface treatment. This work lays solid foundation for future study on the effects of surface treatment on III- and N-polar nanostructured light-emitting-diodes and provides a promising route for the design of nanostructure photonic devices.