A detailed and systematic study of ion implanted MOCVD grown wurtzite gallium nitride (GaN) and aluminum indium nitride (AlInN) is conducted. As-grown samples were characterized using XRD and Hall measurements to check the structural and electrical properties of the samples. Neon (Ne), manganese (Mn) and cerium (Ce) ions were implanted into the materials with different doses in ranges 1014?9x1015, 1014?5x1016 and 3x1014?2x1015cm-2 respectively. Using rapid thermal annealing (RTA) furnace implanted GaN samples were annealed at 800, 850, 900 and 1000oC and implanted AlInN samples were annealed at 750 and 850 oC for lattice recovery and activation of the dopants. Structural and optical characterizations were made using Rutherford backscattering spectroscopy (RBS), X-Ray diffraction (XRD), Photoluminescence (PL), Optical transmission and Raman scattering spectroscopy. Moreover, magnetic characterization of Mn and Ce implanted samples was also carried out with vibrating sample magnetometer (VSM) and superconducting quantum interference device (SQUID).