A computer-implemented method, computer program product and prototyping platform creates a design blueprint for a substrate-based microfluidic device. A design and prototyping platform receives at least one blueprint parameter and at least one constraint associated with a proposed substrate-based microfluidic device including a hydrophilic material and arrangement of a pattern of a hydrophobic material. The platform determines an arrangement of a plurality of microfluidic device elements as candidates for implementation of the proposed substrate-based microfluidic device and outputs a design blueprint of the proposed substrate-based microfluidic device.