We solve the Ginzburg-Landau equations for to study the vortex configurations in a superconducting prism with a square array of pillars or holes in the presence of a uniform applied magnetic field. The presence of the pillars (holes) changes the vortex structures in the superconducting prism considerably. We calculate magnetization, free energy and vorticity curves, which shows the transition between different vortex configurations as a function of magnetic fields.