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A field emission microscope (FEM) is a useful tool for investigating molecular surface structures. Conventional FEMs suffer from poor image contrast level and low sensitivities when low-energy electron beams are applied. In this article, a new anode material is employed to improve the FEM imaging performance. We demonstrate that the device has the capability of clearly capturing images of facet boundaries of crystal structures at the tip of a zinc oxide (ZnO) nanowire as defect sites on a Polymethyl methacrylate (PMMA) film that is exposed to electron beams. The clear image of facet boundaries has not been reported in conventional FEM images.