We investigate the growth behavior and microstructure of Ge self-assembled islands of nanometer dimension on Si (0 0 1) substrate patterned with hexagonally ordered holes of similar to 25 nm depth, similar to 30 nm diameter, and similar to 7 x 10(10) cm(-2) density. At 9 angstrom Ge coverage and 650 degrees C growth temperature, Ge islands preferentially nucleate inside the holes, starting at the bottom perimeter. Approximately 14% of the holes are filled by Ge islands. Moire fringe analysis reveals partial strain relaxation of about 72% on average, which is not uniform even within a single island. Crystalline defects Such as dislocation are observed from islands smaller than 30 nm. Increased Ge coverage to 70 angstrom forms larger aggregates of many interconnected islands with slightly increased filling factor of about 17% of the holes. Reducing the growth temperature to 280 degrees C results in much higher density of islands with a filling factor of about 80% and with some aggregates. The results described in this report represent a potential approach for fabricating semiconductor quantum dots via epitaxy with higher than 10(10)cm(-2) density. (c) 2006 Elsevier B.V. All rights reserved.