Gallium nitride layers were deposited on high-pressure-grown GaN substrates containing planar defects. The layer growth above the defects was disturbed and the layer contained terraces. The terraced region was investigated by the molten-bases defect-selective etching (DSE), atomic force microscopy (AFM), and transmission electron microscopy (TEM) methods. The AFM measurement showed significant differences in atomic steps densities in different parts of the layer. The TEM investigation revealed the presence of stacking faults and the DSE showed that the substrate planar defect influences the layer growth. The schema of the defect–layer interaction has been proposed.