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The cathodoluminescence in-depth spectroscopy (CLIS) technique is applied to GaN-based and GaAs-based structures as a new method of non-destructive in-depth and in-plane characterization. Here, a plot of CL intensity vs. acceleration voltage is defined as the CLIS spectrum, and it is analyzed on computer. Detailed recombination dynamics for band edge emission and yellow luminescence in GaN and AlGaN/GaN materials was clarified by comparing experimental and theoretical CLIS spectra. The method was also successfully applied to in-depth and in-plane characterization of an AlGaAs/GaAs three-dimensionally inter-crossing quantum wire structure, giving information on geometry and alloy composition.