Three-dimensional microstructures of a crystal with epitaxially grown silicon-carbide (3C-SiC) layers were analyzed with a scanning nuclear microprobe combined with a RBS channeling technique. SiC layers were epitaxially grown on a Si crystal substrate by the chemical vapor deposition (CVD) method. By using a 1.6 MeV proton microbeam of 4 μm diameter and focusing angle 0.2°, channeling contrast maps along the <100> crystal axis were obtained. Several anomalously grown nonchanneling regions with a mean diameter of 30 μm were observed in a high-quality crystalline field. These regions were found to have columnar structures from a depth profile analysis. The RBS spectrum showed that stoichiometry of these regions was the same as that in the remaining normal crystal. Elemental maps and depth profiles at the ohmic electrode and the field oxide of the SiC MOS diode were observed by PIXE, RBS and NRA methods using proton, He + and deuteron microbeams, respectively.