A study of the influences of embedding artificial structures in a microfluidic device for CE with a free buffer solution is presented. Compared with conventional slab-gel electrophoresis, three major additional effects on the overall system performance are identified when sub-micron pillar arrays are integrated into a standard CE microsystem. Since DNA molecules have to migrate in-between and interact with the pillars, pillar geometry is first demonstrated to have a direct impact on the DNA motion pattern. Electric field re-distribution is another inevitable outcome when features of sub-micron dimensions are placed inside a microchannel. This effect is verified by a numerical simulation tool. Furthermore, the integration of the closely packed sub-micron structures dramatically increases the surface to volume ratios in the microfluidic device and therefore generates a large EOF. The consequence of these additional influences implies a complexity in the measured DNA velocity and indicates that careful considerations have to be taken when these devices are used for DNA electrokinetics study or electrophoresis theory re-examination.