Experimental studies on patterning hexagonal Ge nanostructures have been conducted on Si substrates through deposition of Ge with colloidal particles as a mask. The deposited Ge thin film possesses, according to the X-ray diffraction measurements, in plane texture, being epitaxial and aligned with the (111) Si substrate. The size distribution of the patterned Ge nanostructures is narrow, as indicated by the atomic force microscopy and scanning electron microscopy measurements. We have obtained Ge nanostructures with lateral dimension of 490 nm (height 12 nm), 200 nm (height 6 nm) and 82 nm (height 6 nm) by using different sizes of polystyrene spheres. We have performed in depth studies of the Ge nanostructures’ behavior due to thermal and rapid thermal post-annealing processes. FT micro-Raman spectroscopy shows that there is no Si intermixing during the annealing process. In order to quantify the changes in the height and lateral dimension, we have performed atomic force microscopy and white light interferometry analysis. The changes in shape and the decrease in the area of a cross-section of Ge nanostructure will be discussed in respect to similar results shown in the literature for Ge thin films during the annealing process.