We have developed a nanoprobe-assisted bottom-up technique that allows to fabricate site-controlled quantum dots (SC-QDs), using a specially designed atomic force microscope probe, referred to as the Nano-jet Probe (NJP). Beginning with the fabrication of regular QD arrays by using the NJP, we vertically aligned self-assembled InAs QDs using the strain-induced stacking method and produced assembled QD stacks. In order to improve the optical property of the SC-QDs, an AlGaAs barrier layer was introduced in the spacer layer of the stacked structures. The photoluminescence measurements of the fabricated structures revealed that they had good crystallographic qualities. (C) 2008 Elsevier B.V. All rights reserved.