Described herein is a method of designing micro-fluidic devices. A target cost function based on device design parameters is chosen. The performance of one or more design candidates is run in a simulation model. A design candidate with a cost function closest to the target cost function is chosen and modified in an optimization routine to provide a modified design candidate having modified device design parameters. The cost function for the modified initial design candidate is computed, and when the modified design candidate has a computed cost function that meets the target cost function, optimized device design parameters of an optimized device design are obtained. Additional optimization iterations may be performed as needed to arrive at an optimized device design. A micro-fluidic device based on the optimized device design is manufactured.