Understanding tissue engineering using a bottom-up approach has been hindered by technical limitations because no platform can demonstrate the controlled formation of a heterogeneous population of cells in microscale. Here, we demonstrate hierarchical shape-by-shape assembly of virus-laden particles into larger ones to transfect two different genes on the seeded cells. We show that smaller daughter particles with different sizes and shapes can be assembled into the matching indentations of larger parent particles with different sizes and shapes. Then, we transfected a population of cells with two different gene-transfecting viruses, each of which was laden on the parent or daughter particles.