Self-assembly of colloidal spheres onto patterned (e.g., lithographically modified [1]) substrates is a promising approach to prepare complex 3D geometries (e.g., assemble colloidal spheres into square pyramidal shapes[2]) that can not be produced by self-assembly of colloidal spheres on flat substrates. Generally self-assembly alone is restricted to the formation of close-packed 2D and 3D arrays of colloidal particles and does not lead to more complex lattice types and geometries. A certain degree of control over colloidal self-assembly has been achieved through external electric[3] or intense optical fields[4] and by manipulating the interaction potential[5]. Here we demonstrate a simple scheme that combines two self-assembly steps and electrochemical deposition to produce patterns of ordered arrays of spheres with controlled spacing and eventually isolated metallic arrays of spherical cavities.