This paper reports the formation of Ge nanoclusters in a multi-layer structure consisting of alternating thin films of Ge-doped silica glass and SiGe, deposited by plasma-enhanced chemical vapor deposition (PECVD) and post annealed at 1100 °C in N2 atmosphere. We studied the annealed samples by transmission electron microscopy (TEM) and Raman spectroscopy. As-deposited and annealed samples were analyzed by secondary ion mass spectroscopy (SIMS). TEM investigation shows that Ge nanoclusters were formed in the as-deposited SiGe layer and the SiGe layer was transformed into a silicon dioxide layer embedded with Ge nanoclusters after annealing. These nanoclusters are crystalline and varied in size. There were no clusters in the Ge-doped glass layer. Raman spectra verified the existence of crystalline Ge clusters. The positional shift of the Ge vibrational peak with the change of the focus depth indicates that the distribution of the stress applied to the Ge clusters varies with depth. SIMS measurements show clearly the dramatic O increase in the as-deposited SiGe layer after annealing. The creation of Ge nanoclusters by the combination of PECVD and annealing makes possible the application in complicated waveguide components.