In this work, a novel approach has been implemented to investigate the submicron (30nm spatial resolution) structural and optical properties of bulk GaN, InGaN/GaN Multiple Quantum Well (MQW), p-typle AlGaN capped MQW, and full Light Emitting Diode (LED) as-grown structures by stopping the Metal Organic Chemical Vapor Deposition (MOCVD) process at various points during the growth. 4 pair or 6 pair of 2.6nm In0.14Ga0.86N/10nm GaN MQW structures have been grown at same well and barrier temperature (at 760oC), and at different well and barrier temperature (well at 760oC and barrier at 860oC). For the first time these structures have been analyzed layer by layer using high resolution Cathodoluminescence (CL) system. This technique allowed independent study of structural and carrier confinement effects of each layer on subsequent layers. Together with other characterization techniques, this novel approach can allow critical improvements in future LED development. Owing to the ability of the CL system to study the luminescence properties in the vertical axis by changing the electron beam voltage, the nonradiative recombination centers (NRRCs) and radiation fluctuations beneath the surface were studied as a function of film depth. Pits and dislocations in bulk GaN and V-pits in MQW were shown to be NRRCs. Luminescence fluctuations, at about 30nm spatial resolution, in MQW emission wavelength was observed in CL images and correlated to local bandgap variation. InGaN/GaN MQW layers revealed double peak emission at 2.74eV and 2.82eV. Optical microscopy, Atomic Force Microscopy (AFM) and its electrical modules, X-ray diffraction (XRD), photoluminescence (PL), electroluminescence (EL), time resolved PL (TRPL), Scanning Transmission Electron Microscopy (STEM), and Secondary Ion Mass Spectrometry (SIMS) analysis were performed to investigate the origin of double peak emission. The low energy (LE) emission at 2.74eV was attributed to InGaN/GaN MQWs, and the high energy (HE) emission at 2.82eV to nanostructures formed surrounding the (VGa-ON)2- point defects mainly at the bottom pairs of MQW layer due to the strain relaxation by the point defects and the compositional pulling effect. This O impurity introduced HE emission decreases the quantum efficiency of the MQW structure and deteriorated the device performance by forming leakage paths. It was observed that O impurity incorporation was enhanced by defective nature of the films and low growth temperature. It was shown that higher temperature growth of GaN quantum barriers at 860oC eliminated the double peak InGaN emission.