Scanning tunneling microscopy and noncontact atomic force microscopy have been used to observe germanium growth on Si(001) and Si(111). The atomically resolved images provide invaluable information on heteroepitaxial film growth from the viewpoints of both industrial application and basic science. We briefly review the history of characterizing heteroepitaxial elemental semiconductor systems by means of scanning probe microscopy (SPM), where the Stranski–Krastanov growth mode can be observed on the atomic scale:the detailed phase transition from layer-by-layer growth to three-dimensional cluster growth was elucidated by the use of SPM. In addition, we comment on the potential of SPM for examining the spectroscopic aspects of heteroepitaxial film growth, through the use of SPM tips with well-defined facets.