This paper surveys recent developments in engineering physics approaches ann self-assembly chemistry methodologies for creating 3D photonic crystals and how this has led to in-wafer patterned colloidal crystals. These materials are comprised of single crystal micrometer scale features of silica colloidal crystals that have controlled thickness, area, and orientation and are embedded within a single crystal silicon wafer. Two processes for growing opal-patterned are chips are described, One is based upon microfluidic and the other spin coating driven self-assembly of colloidal silica micro-spheres within a lithographic patterned silicon wafer.