Microtubules (MTs) are highly dynamic polymers distributed in the cytoplasm of a biological cell. Alpha and beta globular proteins constituting the heterodimer building blocks combine to form these tubules through polymerization, controlled by the concentration of Guanosine-triphosphate (GTPs) and other Microtubule Associated Proteins (MAPs). MTs play a crucial role in many intracellular processes, predominantly in mitosis, organelle transport and cell locomotion. Current research in this area is focused on understanding the exclusive behaviors of self-organization 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 mostly unexplored. In this study, we propose a novel swarm engineering framework in modeling rules for these systems, by combining the principles of design with swarm intelligence. The proposed framework was simulated on a game engine and these simulations demonstrated self-organization of rings and protofilaments in MTs. Analytics from these simulations assisted in understanding the influence of GTPs on protofilament formation. Also, results showed that the population density of GTPs rather than their bonding probabilities played a crucial role in polymerization in forming microtubule substructures.