We use a bond-fluctuation Monte Carlo method to study the motion of long polyelectrolytes inside an array of microscopic entropic traps. The molecules are pulled through the array by an electric field and forced into submalecular-size constrictions between the larger trap regions. We numerically solve the Laplace equation inside the structure to obtain realistic field lines for our simulations. We find that the mobility of the molecules increases with molecular size and that the size-separation mechanism relies mainly on the overall deformation of the molecules as they approach the narrow constrictions. We also investigate specific aspects of the separation mechanism, namely the conformational behavior of the molecule, the hernia nucleation process, and the trapping time statistics as a function of molecular size and field strength. Our simulation results for the mobility, the critical hernia nucleation size, the mean trapping time, and the resolution are consistent with the experimental data and model previously published by Han et al.(1,2) Finally, we predict that such microfluidic structures could be used to separate topoisomers bearing the same molecular size.