Confinement effects on the electromigration of long dsDNA molecules in an array of well-ordered, molecular sized cavities interconnected by nanopores are described. The array was prepared by replicating the structure of a colloidal crystal of microspheres in a polymer matrix. Both conformation and mobility studies show that the electrophoretic behavior of large DNA molecules is distinct from that in gels and other microfabricated sieves, showing a peak in mobility versus electric field, and an inversion in the separation order with field strength. A simple model was proposed to interpret this unexpected observation qualitatively. We conclude that the molecular behavior of DNA can be modified by the combination of entropic effect and electric trapping as a consequence of both unique geometry and conductivity of this cavity array material. This approach provides insights for design and optimization of on-chip molecular sieving structures for rapid separation of long DNA molecules. It may lead to a promising material for manipulation and size fractionation of other biological macromolecules.