Most of the ion implanter is large scale, high acceleration voltage and expensive. For research and development, such a huge implanter is not required. Our motivation is to make desktop type ion implanter for SiC device. We report the fabrication of a compact 100 kV ion implanter. In order to miniaturize the equipment, an ion source, an accelerator tube and a main chamber were vertically arranged. We implanted Argon (Ar) and Nitrogen (N) ions to 6H-SiC substrate and the implanted 6H-SiC substrates were characterized by Fourier Transform Infrared Spectrometer (FTIR), Rutherford Backscattering Spectrometry (RBS) and Secondary Ion Mass Spectrometry (SIMS). In this report, concept of desktop ion implanter, evaluation of implanted substrate and its device application are presented. In order to characterize capability, with using the newly made compact ion implanter, it was possible to make implantation on SiC to get amorphous layer suitable for deices.