The present invention relates to methods and systems for optimization of dilution of a viscous starting material to isolate and/or concentrate the product of interest from the starting source material such that the process minimizes the volume of diluent and the total volume of the waste stream generated during the process as well as maximizing the yield of desired product. The system employs cross-flow filtration modules with sub-channels that are equidistant to the inlet and outlet of said modules and such modules are characterized by optimal channel height, optimal transmembrane pressure, etc., which are selected in order to achieve the best combination of product quality and production yield.