The first step in synthesizing a model film morphology via a surface-driven hierarchical assembly process is presented. The goal of the hierarchical assembly is the control of the morphology of complex molecular layers for the investigation of fundamental processes in organic solar cells. Using a focused ion beam (FIB) with Ga+ ions at 30 keV, the surface of highly oriented pyrolitic graphite (HOPG) is patterned with an array of local amorphous carbon ellipsoid spots (ACES), which provide preferential nucleation lines at their perimeter, and thus are instrumental in the control of fullerene island growth. On the undamaged surface regions outside the ACES pattern the fullerene island growth is unperturbed, and presents the well-known combination of round and fractal island shapes. The fullerene deposition at the periphery of the ACES pattern, which is characterized by single ion impact defects, results in stunted, smaller and irregular islands. Inside the ACES array, the C60 island growth is controlled by the shape of the ACES and is constrained to lobes which form around each ACES spot. The array and C60 lobe morphology and geometry are characterized and a subsequent understanding of the C60 diffusion fields and nucleation lines within the array is discussed.