Controlling the morphology and composition of semiconductor nano- and micro-structures is crucial for fundamental studies and applications. Here, Si-Ge semiconductor nanostructures were fabricated using photolithographically defined micro-crucibles on Si substrates. Interestingly, the nanostructure morphology and composition of these structures are strongly dependent on the size of the liquid–vapour interface (i.e., the opening of the micro-crucible) in the CVD deposition step of Ge. In particular, Ge crystallites nucleate in micro-crucibles with larger opening sizes (3.74–4.73 μm2), while no such crystallites are found in micro-crucibles with smaller openings of 1.15 μm2. This interface area tuning also results in the formation of unique semiconductor nanostructures: lateral nano-trees (for smaller openings) and nano-rods (for larger openings). Further TEM imaging reveals that these nanostructures have an epitaxial relationship with the underlying Si substrate. This geometrical dependence on the micro-scale vapour–liquid–solid (VLS) nucleation and growth is explained within a dedicated model, where the incubation time for the VLS Ge nucleation is inversely proportional to the opening size. The geometric effect on the VLS nucleation can be used for the fine tuning of the morphology and composition of different lateral nano- and micro-structures by simply changing the area of the liquid–vapour interface.