We report the self-organization of organic nanodots with high crystallinity during the growth of organic heterostructures of Di-indenoperylene (DIP) onto copper-hexadecafluorophthalocyanine (F16CuPc), donor and acceptor molecules, respectively. The process is related to the Stranski-Krastanov growth mode, which is accompanied by a novel type of structural reconstruction of the underlying organic film. This reconstruction affects three monolayers adjacent to the organic interface. In spite of the close resemblance to the formation of semiconductor nanostructures for inorganic heteroepitaxy, the present results conclusively demonstrate a distinctly different growth mechanism for organic heteroepitaxy whose understanding demands further theoretical studies.