In this work, we propose a framework that derives the configuration of an artificial, compartmentalized, cell-like structure in order to maximize the yield of a desired output reactant given a formal description of the chemistry. The configuration of the structure is then used to compile G-code for 3D printing of a microfluidic platform able to manufacture the aforementioned structure. Furthermore, the compiler output includes a set of pressure profiles to actuate the valves at the input of the microfluidic platform. The work includes an outline of the steps involved in the compilation process and a discussion of the algorithms needed for each step. Finally, we provide formal, declarative languages for the input and output interfaces of each of these steps.