We report on modeling and experimental studies of the synthesis of opaque microparticles made via stop-flow lithography. Opaque magnetic beads and UV-absorbing dyes incorporated into hydrogel microparticles during synthesis changed the height and the degree of cross-linking of the polymer matrices formed. The effect of the concentration of these opaque materials on the particle height was determined experimentally and agreed well with model predictions based on the photopolymerization process over a wide range of UV absorbance. We also created particles with two independent anisotropies, magnetic and geometric, by applying magnetic fields during particle synthesis. Our work provides a platform for rational design of lithographic patterned opaque particles and also a new class of structured magnetic microparticles.