For the last few years much work has been done in the field of semiconductors doped with different rare earth ions (RE) due to their interesting optical properties. By changing the RE one can obtain luminescence covering the whole visible light spectrum. Due to its suitable physical, chemical and mechanical properties GaN seems to be promising material as a host for RE. As a wide and direct band gap semiconductor significantly reduces thermal quenching of the RE luminescence. Ion implantation is one of the techniques that can be used for doping GaN with different RE ions. It was shown that GaN is a very resistant material to irradiation damage, nevertheless during the implantation a lot of damage is created in the implanted areas. Using transmission electron microscopy (TEM) we carry out a structural characterization of GaN implanted with Tm ions. Our aim is to determine optimal conditions of implantation process and further annealing. We present results from samples implanted with different energies (150-300 kV), fluences (0.2-2.2x10¹⁵ Tm/cm²) and temperatures (20-500^oC). The influence of the dose, energy, temperature and the annealing on the structural quality of the layers will be discussed in detail.