In this paper, a sandwich structure comprising a SiO2 capping layer, amorphous Germanium (a-Ge) nanodots (NDs), and a pit-patterned Silicon (Si) substrate is developed, which is then annealed by utilizing a pulsed ultraviolet excimer laser in order to fabricate an array of pure, single crystal Ge NDs at room temperature. A wide bandgap SiO2 capping layer is used as a transparent thermally isolated layer to prevent thermal loss and Si–Ge intermixing. The two-dimensional pit-patterned Si substrate is designed to confine the absorbed laser energy, reduce the melting point, and block the surface migration of the Ge. After optimizing the laser radiation parameters such that the laser energy density is 200 mJ cm−2, the laser annealing period is 10 s, and the number of laser shots is 10, pure, single crystal Ge NDs that have both a regular arrangement and a uniform size distribution are obtained in the pits of the Si substrates. The Raman spectrum shows a highly symmetric Ge transversal optical peak with a full width at half maximum of 4.2 cm−1 at 300.7 cm−1, which is close to that of the original Ge wafer. In addition, the high-resolution transmission electron microscopy image for the Ge NDs and the corresponding selected area electron diffraction pattern shows a clear single crystalline structure without any impurities.