© 2018 The Author(s). With rapid advances occurring in terahertz (THz) radiation generation techniques, the interaction between matter and intense THz fields has become an important research topic. Among different types of THz radiation sources, the free electron laser (FEL) is a promising experimental tool that is expected to pave the way for new forms of material processing, control of phase transitions, and serve as a test bench for extreme operating conditions in high-speed small-size electrical and magnetic devices through the exploitation of strong THz electrical and magnetic fields without the presence of interband electronic excitation. In the current work, we irradiated Ge2Sb2Te5 phase change memory material with intense THz pulse trains from an FEL and observed THz-induced surface changes due to damage as a precursor to ablation and the formation of fine surface undulations whose spatial period is comparable to or slightly smaller than the wavelength of the excitation THz pulses in the material. The formation of undulations as well as the fact that no significant thermal effect was observed below the volume expansion threshold suggests that THz-induced effects mainly contributed to the observed changes. To the best of our knowledge, this is the first experimental observation of THz-induced undulations (so-called "LIPSS"), which are of potential importance for laser material processing.