Synthetic helical micro/nano structures capable of swimming in low Reynolds number fluid are foreseen to change many aspects in medicine by enabling targeted therapy and diagnosis. This paper aims to obtain the optimised design of the helical swimmers for biomedical applications. A finite element analysis was carried out to characterise the mechanical behaviour of different micro helical structures made from a range of biocompatible/degradable metals including gold, silver, zinc, magnesium and polylactic acid (PLA). Taguchi method was utilised in order to find the most robust geometrical design of a helical swimmer. Finally, the drag forces acting on different helical designs swimming in low Reynolds number fluid were calculated. The optimised design is the one yield the highest spring stiffness. It was found that among the selected materials, the design yielded excellent mechanical properties with the best spring stiffness has a pitch length of 80 μm, 3 revolutions, an outer diameter of 110 μm, a thickness of 15 μm and made of zinc.