The surface morphological characteristics of wet chemical etched GaN layers grown at different temperatures on (0 0 0 1) sapphire substrates by Chloride-Vapor Phase Epitaxy (Cl-VPE) have been studied using optical microscope. Significant surface morphology changes have been observed in correlation to the growth temperature and etching time. Also optical properties of the as grown and high-energy silicon (Si) ion irradiated gallium nitride (GaN) epilayers were studied using monochromatic ellipsometry. The effect of ion fluences on the refractive index of the GaN has been investigated and it has been found to decrease with an increase of ion fluence. This decrease is attributed to irradiation-induced defects and polycrystallization which plays an important role in determining the optical properties of silicon (Si) ion irradiated GaN layers.