Using computational modeling, we simulate the fluid-driven motion of microcapsules on patterned surfaces to establish guidelines for creating simple microfluidic devices for bioassays and multistage chemical reactions. The microcapsules, which consist of an elastic shell and an encapsulated fluid, model biological cells or polymeric particles. We focus on patterned substrates that encompass chemically adhesive and mechanically compliant domains. By probing the interactions between the microcapsules and these patterned surfaces, we determine the factors that control the movement of the capsules along the substrates. Using this information, we optimize the arrangement of the adhesive and compliant surface domains to create robust systems that effectively discriminate between various soft particles moving through the microchannels and "autonomously" direct certain species to specific locations. These findings could facilitate the fabrication of low-cost, portable microfluidic devices for sorting cells or performing fundamental chemical studies.