While producing comparable efficiencies and showing similar properties when probed by conventional techniques, such as Raman spectroscopy, photoluminescence, and x-ray diffraction, two thin-film solar-cell materials with complex structures, such as quaternary compound Cu 2 ZnSnSe 4 (CZTSe), may, in fact, differ significantly in their microscopic structures. In this work, laser-induced-modification Raman spectroscopy coupled with high spatial resolution and high-temperature capability is demonstrated as an effective tool to reveal the existence of microscopic scale variations between nominally similar alloys and, thus, to obtain additional structure information beyond what the conventional characterization techniques can offer. Specifically, CZTSe films prepared by sputtering and coevaporation methods that exhibit similar Raman and XRD features are found to behave very differently under high laser power and high-temperature Raman probe because the difference in their microscopic structures leads to different structure modifications in response to the external stimuli, such as light illumination and temperature. They are also shown to undergo different degrees of plastic changes and have different thermal conductivities as revealed by spatially resolved Raman spectroscopy. This technique provides a convenient way to assess and compare materials and provides complementary information for other structural characterization techniques, such as TEM and XRD.