SiC is a material used in two future energy production technologies, firstly as a photovoltaic layer to harness the UV spectrum in high efficient power solar cells, and secondly as a diffusion barrier material for radioactive fission products in the fuel elements of the next generation of nuclear power plants. For both applications, there is an interest in the implantation of reactive and non-reactive ions into SiC and their effects on the properties of the SiC. In this study 360 keV Ag+, I+ and Xe+ ions were separately implanted into 6H–SiC and in polycrystalline SiC at various substrate temperatures. The implanted samples were also annealed in vacuum at temperatures ranging from 900 °C to 1600 °C for various times. In recent years, there had been significant advances in scanning electron microscopy (SEM) with the introduction of an in-lens detector combined with field emission electron guns. This allows defects in solids, such as radiation damage created by the implanted ions, to be detected with SEM. Cross-sectional SEM images of 6H–SiC wafers implanted with 360 keV Ag+ ions at room temperature and at 600 °C and then vacuum annealed at different temperatures revealed the implanted layers and their thicknesses. A similar result is shown of 360 keV I+ ions implanted at 600 °C into 6H–SiC and annealed at 1600 °C. The 6H–SiC is not amorphized but remained crystalline when implanting at 600 °C. There are differences in the microstructure of 6H–SiC implanted with silver at the two temperatures as well as with reactive iodine ions. Voids (bubbles) are created in the implanted layers into which the precipitation of silver and iodine can occur after annealing of the samples. The crystallinity of the substrate via implantation temperature caused differences in the distribution and size of the voids. Implantation of xenon ions in polycrystalline SiC at 350 °C does not amorphize the substrate as is the case with room temperature heavy ion bombardment. Subsequent annealing of the implanted polycrystalline samples leads to increased thermal etching effects such as grain boundary grooving. Damage due to channelling (or non-channelling) in the different crystallites resulted also in differences in thermal etching in the crystallites.