We report here swift heavy ion (SHI) irradiation induced effects on structural and surface properties of III-nitrides. Tensile strained Al(1-x)InxN/GaN Hetero-Structures (HS) were realized using Metal Organic Chemical Vapour Despotion (MOCVD) technique with indium composition as 12%. Ion species and energies are chosen such that electronic energy deposition rates differ significantly in Al(1-x)InxN and are essential for understanding the ion beam interactions at the interfaces. Thus the samples were irradiated with 80 MeV Ni6+ and 100 MeV Ag7+ ions at varied fluence (1×1012 and 3 ×1012 ions/cm2) to alter the structural properties. Under this energy regime, the structural changes in Al(1-x)InxN would occur due to the intense ultrafast excitations of electrons along the ion path. We employed different characterization techniques like High Resolution X- ray Diffraction (HRXRD) and Rutherford back scattering spectrometry (RBS) for composition, thickness and strain. HRXRD and RBS experimental spectra have been fitted with Philip’s epitaxy SIMNRA code, which yields thickness and composition from compound semiconductors. The surface morphology of pristine and irradiated samples is studied and compared by Atomic Force Microscopy (AFM).