Scanning tunnelling microscopy (STM) study and modification of hydrogen (H)-passivated Ge(100) surfaces have been investigated. Thermal oxidation procedures were used to minimise surface roughness. Ge samples were passivated in HF solution after thermal oxidation. STM and atomic force microscope (AFM) imaging showed that, using HF etching after thermal oxidation, we can obtain a natural H-passivatedtopographically and chemically flat Ge(100) surface. The root-mean-square (rms) roughness ofa H-passivatedGe(100) surface measured both by STM and AFM is less than 2 Å. Electric properties of H-passivatedGe(100) surfaces were studied by scanning tunnelling spectroscopy (STS) in nitrogen ambient. STS showed that the H-passivated Ge surfaces were not pinned. Modification on H-passivated Ge(100) surfaces was carried out using STM by applying an electric voltage between the sample and tip in air. Modified features were characterised by STM and AFM imaging. On the H-passivated Ge(100) surfaces, stable, low-voltage, nanometer-scale modified features can be produced.