In this work, a well-controllable, direct-write, resistless, and crystallinity-retaining etching process for germanium using a focused electron beam with nanometer resolution has been developed. This process allows for precise, local, and efficient removal of germanium from a surface without showing any spontaneous etching effects. This focused electron beam induced etching process of germanium substrates employs pure chlorine gas as etchant. The presented process was carried out in a conventional scanning electron microscope equipped with a custom-tailored gas injection system. The etch rate of this etching process was observed to be up to 0.32 μm3 min−1 or 12 nm min−1 for an area of 1.5×1.5 μm2. The influence of various etching parameters such as electron beam current, acceleration voltage and chlorine gas flow on the etch rate as well as the shape of the etch pits have been studied systematically by atomic force microscopy analysis. It is demonstrated that etching of amorphous germanium films can be performed significantly faster (∼8 times) than etching of crystalline germanium. Finally, a comparison between silicon etching and germanium etching by chlorine is presented.