Precise, size-selective assembly and sorting are demonstrated in a low-cost system using manufacturable, replicated polymer templates to guide the assembly. Surface interactions between microscale objects and an assembly template are combined with fluid forces to drive site-selective organization of objects onto the template. Although controlling the organization of deformable objects on deformable surfaces offers a key tool for biological applications, the deformability can potentially interfere with the process that drives size selectivity. Theoretical models of the polymer assembly system were created to predict when selectivity will fail in deformable systems and were validated by comparison with experiments. Selective template-driven assembly of polystyrene microspheres on PDMS templates replicated from silicon masters was carried out using templated assembly by selective removal (TASR), demonstrating the effectiveness of selective assembly with low-cost, manufacturable materials and processes. The assembly of polystyrene microcomponents on PDMS shows high assembly yields and effective selectivity, in agreement with models.