We report a simple method for controlled embedment of polymer components within injection molded polymer surface structures. The structures were micro-sized channels and pits with various step-size ratios. Two types of affinity differences were created between the top and the bottom of the structures which allowed a selective deposition of embedded components. The dissolved embedding components were spread onto the sample by spin coating. Solvent and thermal annealing then facilitated the phase separation of them from the upper surface and segregated them into the structure bottoms. Our results show that with the optimal step-size ratio, mobilized polymer components are capable of traveling across a leveled structure top. With the thiol customized affinity difference, the proposed method is applicable for the embedment of special components, such as nanoparticles, cells and biomolecules, in addition to polymer components.