Structural and optical properties of hybrid structures with multiple layers of semiconductor InAs/AlGaAs quantum dots and indium clusters on the surface are investigated. Before we have shown that in such hybrid structures strong exciton-plasmon interaction takes place. It results in non-radiative energy transfer to a large quantum dot that acts as an acceptor and the consequent enhancement of the long-wavelength photoluminescence that was obtained in our experiments. Here, we demonstrate vertical alignment of indium clusters over quantum dots with direct method of scanning transmission electron microscopy. Analysis of photoluminescence spectra reveals that the main contribution to exciton-plasmon interaction is provided by the upper layer of quantum dots located near metal particles.