3D InGaN/GaN microstructures grown by metal organic vapor phase epitaxy (MOVPE) and molecular beam epitaxy (MBE) have been extensively studied using a range of electron microscopy techniques. The growth of material by MBE has led to the growth of cubic GaN material. The changes in these crystal phases has been investigated by Electron Energy Loss Spectroscopy, where the variations in the fine structure of the N K-edge shows a clear difference allowing the mapping of the phases to take place. GaN layers grown for light emitting devices sometimes have cubic inclusions in the normally hexagonal wurtzite structures, which can influence the device electronic properties. Differences in the fine structure of the N K-edge between cubic and hexagonal material in electron energy loss spectra are used to map cubic and hexagonal regions in a GaN/InGaN microcolumnar device. The method of mapping is explained, and the factors limiting spatial resolution are discussed.