Epitaxial AlGaN/GaN layers grown by MBE on SiC substrates were irradiated with 150 MeV Ag ions at a fluence of 5×1012 ions/cm2. AlGaN/GaN MQWs were grown on Sapphire substrate by MOCVD and irradiated with 200 MeV Au8+ ions at a fluence of 5×1011 ions/cm2 . These samples were used to study the effects of SHI on optical properties of AlGaN/GaN based nano structures. RBS/Channelling strain measurements were carried out at off normal axis of irradiated and unirradiated samples. In as grown samples, AlGaN layer is partially relaxed with a small compressive strain. After irradiation this compressive strain increases by 0.22% in AlGaN layer. Incident ion energy dependence of dechannelling parameter shows E1/2 dependence, which corresponds to the dislocations. Defect densities were calculated from the E1/2 graph. As a result of irradiation defect density increased on both GaN and AlGaN layer. Optical properties of AlGaN/GaN MQWs before and after irradiation have been analyzed using PL. This study shows that SHI increase the confinement effects in the MQWs and intensity of the active layer of the MQWs luminescence is increased by one order. This may be due to the induced strain in GaN and AlGaN layers. Some unwanted yellow luminescence has also been introduced by the SHI possibly due the point defects or defect luminescence from the induced dislocations in GaN bulk epitaxial layers. In this study, we present some new results concerning high energy irradiation on AlGaN/GaN heterostructures and MQWs characterized by RBS/Channelling and PL.