Despite having an excellent infrared optical property, efficient material removal of zinc selenide (ZnSe) is yet to be realized and its defect generation mechanisms during ultra-precision cutting are not fully elucidated. In this study, ultra-precision cutting experiments on polycrystalline ZnSe were conducted by considering various cutting parameters and utilising surface topography, chip morphology, cutting force, and X-ray diffraction data to investigate its surface generation mechanisms, which were further augmented by molecular dynamics simulations to analyse the generation and suppression of surface defects. The results revealed the presence of irregular microstructures on the surface of polycrystalline ZnSe, arising from variations in material rebound owing to differing grain orientations, as well as micron-sized craters located at grain boundaries and submicron-sized pits within individual grains. Increasing the cutting speed facilitated instantaneous grain fractures, thus preventing grain peeling and effectively suppressing the generation of micron-sized craters and material rebound. Although the use of a negative rake angle on the tool suppressed the generation of micron-sized craters, it introduced a proliferation of burrs that was detrimental to the surface finish. These findings provide valuable insights for optimising the ultra-precision machining process and enhancing the surface quality of brittle polycrystalline ZnSe.