Microtubules are highly dynamic polymers distributed in the cytoplasm of a biological cell. Alpha and beta tubulins combine to form these tubules through polymerization, controlled by the concentrations of GTPs and MAPs. These play a crucial role in many intra cellular processes, predominantly in mitosis, organelle transport and cell locomotion. Current research in this area is primarily focused on understanding these exclusive behaviors of organization of tubules and their association with different MAPs through organized laboratory experiments. However, the intriguing intelligence behind these tiny machines resulting in complex self-organizing structures is largely unexplored. Understanding this can support researchers in validating many hypotheses in quicker and cost-effective ways. On these lines, we propose a novel swarm engineering framework in modeling rules for these systems, by convolving the principles of design with swarm intelligence. The proposed rules were simulated on a game engine and this approach demonstrated self-organization of rings and protofilaments.