We investigate the assembly of block copolymer-nanoparticle composite films on chemically nanopatterned substrates and present fully three-dimensional simulations of a coarse grain model for these hybrid systems. The location and distribution of nanoparticles within the ordered block copolymer domains depends on the thermodynamic state of the composite in equilibrium with the surface. Hierarchical assembly of nanoparticles enables applications in which the ability to precisely control their locations within periodic and nonregular geometry patterns and arrays is required.