The structure and chemistry of clean GaN surfaces and InGaN thin films and nanostructures grown by metal organic vapour pressure epitaxy (MOVPE) has been studied by means of X-ray photoemission spectroscopy, low-energy electron diffraction as well as scanning tunneling microscopy (STM) and transmission electron microscopy. Thermal annealing strongly improves the cleanliness of samples after dry nitrogen transfer and related exposure to residual oxygen. Nitrogen plasma assisted cleaning is shown to successfully further remove carbon contaminations, while Ga deposition with subsequent desorption to is shown to be superior for an enhanced reduction of surface oxygen. Using STM, the surface morphology has been studied in dependence on major growth parameters at various stages of InGaN MOVPE growth. The formation of nano-islands is reported for different growth conditions. By means of microphotoluminescence measurements, we find samples to show strong photoluminescence from quantum-dot-like structures, however, the corresponding growth front is found to be rather flat throughout InGaN deposition. This leads to the conclusion that the formation of quantum dots does not proceed in a Stranski-Krastanov-like fashion but most likely during overgrowth.Scanning tunneling micrograph and height profile of 3.9 nm InGaN grown by MOVPE at 700 8C, after growth interruption and 1 min post-growth annealing at the growth temperature. The surface exhibits a two-dimensional islands morphology.