Site-specific focused ion beam milling procedures are used to prepare cross-sectional TEM sample foils through a range of epitaxial GaN thin films. The high threading defect densities associated with heteroepitaxial GaN/sapphire prohibit the unambiguous identification of hillock nucleation events. Inversion domains are, however, identified at the core of hillocks formed on CVD grown GaN on N-polar bulk GaN substrates. It is considered that remnant contamination from the KOH chemomechanical polishing procedure is responsible for the inversion domain nucleation.