A scalable method for site-selective, directed self-assembly of colloidal opals on topologically patterned substrates is presented. Here, such substrate contains optical waveguides which couple to the colloidal crystal. The site-selectivity is achieved by a capillary network, whereas the self-assembly process is based on controlled solvent evaporation. In the deposition process, a suspension of colloidal microspheres is dispensed on the substrate and driven into the desired crystallization sites by capillary flow. The method has been applied to realize colloidal crystals from monodisperse dielectric spheres with diameters ranging from 290 to 890 nm. The method can be implemented in an industrial wafer-scale process.