Self-organization sites of InAs quantum dots (QDs) are arranged to form three-dimensional (3D) lattices by ultrahigh vacuum in situ processing. In-plane QD arrangement in the 3D lattices is initially defined by site-controlled InAs QD arrays fabricated by a scanning tunneling microscope probe-assisted technique. With the QD arrays used as strain templates, self-organized InAs QDs are vertically aligned by multistacking, resulting in the 3D QD lattices. The photoluminescence from the 3D QD structures is investigated at room temperature.