The microstructure of epitaxially grown self-assembled Ge islands on patterned SiO2/Si substrates was analyzed using high resolution transmission electron microscopy. The Ge islands were grown by molecular beam epitaxy on hexagonally ordered Si hole arrays with ∼25nm diameter and ∼40nm center-to-center distance, which are covered by 30 nm thick SiO2 mask layer patterned using self-assembled diblock copolymers. The Ge islands nucleate preferentially at the edge of overetched Si surface, and subsequently grow selectively on Si surface as opposed to SiO2 surface with increasing coverage. The lattice planes of some Ge islands are tilted from those of Si substrates. This is believed to be the reason for the observed misalignment of moiré fringes. The diameter of the Ge islands is identical to that of Si holes for large Ge coverage due to the selective growth behavior. These islands are found to have dislocations at the interface with the Si substrate. These results highlight the important microstructural issues and growth behavior of quantum dots on patterned substrates.