The stochastic transport of suspended particles through a periodic pattern of obstacles in microfluidic devices is investigated by means of the Fokker-Planck equation. Asymmetric arrays of obstacles have been shown to induce the continuous separation of DNA molecules of different length. The analysis presented here of the asymptotic distribution of particles in a unit cell of these systems shows that separation is only possible in the presence of a driving force with a non-vanishing normal component at the surface of the solid obstacles. In addition, vector separation, in which different species move, in average, in different directions within the device, is driven by differences on the force acting on the various particles and not by differences in the diffusion coefficient. Monte-Carlo simulations performed for different particles and force fields agree with the numerical solutions of the Fokker-Planck equation in the periodic system.