Abstract The recent development of blue and green light emitting diodes (LED) based on single quantum well structures made from GaN and related materials (AlGaN, InGaN) has created large efforts to optimise the growth methods used in their production. Rutherford Backscattering (RBS), in combination with channeling analysis, is a powerful tool for the quantitative characterization of the depth profile and the crystallinity of such structures. New growth modes, e.g. lateral overgrowth processes, are being rapidly developed. Channeling contrast microscopy (CCM), which employs a focused ion beam in order to obtain laterally resolved channeling yield data, is ideally suited to determine micro structural characteristics, (e.g. defect densities, tilts in lattice planes, strain) of such samples. Here we report results from proton channeling contrast measurements of laterally overgrown GaN thin films. Such measurements require a sub-micron ion beam focus size as well as an highly stable accelerator system, both of which are available at the Research Centre for Nuclear Microscopy at the National University of Singapore, where an ultrastable Singletron accelerator was recently installed.