We investigated the selective growth of germanium into nanoscale trenches on silicon substrates. These nanoscale trenches, the smallest size of which was 50 nm, were fabricated using the state-of-the-art shallow trench isolation technique. The quality of the Ge films was evaluated using transmission electron microscopy. The formation of threading dislocations (TDs) was effectively suppressed when using this deposition technique. For the Ge grown in nanoscale Si areas (e.g., several tens of nanometers), the TDs were probably readily removed during cyclic thermal annealing predominantly because their gliding distance to the SiO2 sidewalls was very short. Therefore, nanoscale epitaxial growth technology can be used to deposit Ge films on lattice-mismatched Si substrates with a reduced defect density.