Design of chemical processes is usually based on rigorous modeling of unit operations. Unfortunately, the use of physically grounded models in biotechnological applications is rare since their design is mainly based on heuristics and experiments. In this work a computer aided design method is presented for modeling of aqueous two-phase extraction of monoclonal antibodies (MAbs). A conventional counter current extractor is compared with a fractional extractor in terms of purity and concentration of MAbs in the extract. The purity of MAbs increased from 85% in the conventional to almost 100% in the fractional extractor.