The effects of thermal annealing and laser beam illumination on the structure of amorphous Se/CdSe multilayers of up to 20 periods and various sublayer thicknesses (3.5, 5, 6.5 and 10 nm) have been studied by measuring the higher frequency (vibrational) Raman spectra. Three Raman bands have been observed in this spectral region at 209 cm −1 (CdSe), 237 cm −1 (Se) and 256 cm −1 (Se). After annealing, the intensity of these bands increases for all amorphous multilayers (AML) samples which, in a first approach, indicates an improvement of interface quality. In AML of thin (<5 nm) sublayers, annealing results in an increased ordering of both Se and CdSe sublayers, while in AML of thicker (>5 nm) sublayers the opposite effect is concluded for Se sublayers, and hardly any change for CdSe ones. A gradual increase of laser power density causes a likewise modification of Raman spectra, which is attributed to crystallization of Se sublayers; in similar low temperature (25 K) experiments (using even higher laser power densities) there is no indication of substantial crystallization, implying that the latter is mainly a thermal effect. From the threshold for crystallization, we observed that the structural stability of Se/CdSe AML is better, the smaller the sublayer thickness, an important result for electrophotographic applications.