The Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) state is the superconducting phase for which the Cooper pairs have a non-zero total momentum, depending on the splitting of the Fermi surface sheets for electrons with opposite spin. In infinite systems the momentum is a continuous function of the temperature. In this paper, we have shown how the finite size of the system, through the discretized geometry of the Fermi surface, affects the physical properties of the FFLO state by introducing discontinuities in the Cooper pair momentum. Our calculations in an isotropic system show that the superconducting state with two opposite Cooper pair momenta is more stable than state with one momentum also in nano-size systems, where finite size effects play a crucial role.