In this chapter, we address a less classical problem that illustrates the user-friendly yet effective framework provided by FreeFEM to solve a shape optimization problem with mesh modifications combined with the powerful interior point method IpOpt. Based on the mathematical framework introduced in Chap. 1 and following the numerical tools illustrated in Chap. 2 , we consider the optimal design problem of a microfluidic swimmer’s membrane consisting of maximizing its velocity in a given direction. We treat the membrane as a moving lower boundary of a domain where a Stokes fluid evolves and we want to maximize the fluid velocity at the free surface, by imposing constraints on the length and curvature of the boundary.