Complementary nondestructive electron probe methods were used for characterization of semiconductor multilayer structures. We used cathodoluminescence and electron probe microanalysis for studying laser heterostructures based on GaAs/AlGaAs/InGaAs/GaAs and InGaN/GaN. Our latest investigation showed the possibility of measuring the composition of buried layers and determining the composition of thin nanoscale layers by electron probe microanalysis. Simultaneous use of local cathodoluminescence is very useful for defect study in bulk semiconductors, epilayers, and multilayer heterostructures. This method allows characterization of charge-carrier transport properties and diffusion length in multilayer structures, using the variation of the electron beam energy and calculation of the electron penetration depth.