Laser lift-off and bonding has been demonstrated as a viable route for the integration of III-nitride opto-electronics with mainstream device technology. A critical remaining question is the structural and chemical quality of the layers following lift-off. In this paper, we present detailed structural and chemical characterization of both the epitaxial layer and the substrate using standard transmission electron microscopy techniques. Conventional diffraction contrast and high resolution electron microscopy indicate that the structural alteration of the material is limited to approximately the first 50 nm. Energy dispersive electron spectroscopy line profiles show that intermixing is also confined to similar thicknesses. These results indicate that laser lift-off of even thin layers is likely to result in materials suitable for device integration. Additionally, because the damage to the sapphire substrate is minimal, it should be possible to polish and re-use these substrates for subsequent heteroepitaxial growths, resulting in significant economic benefits.