A novel design approach for optimizing the shape of microfabricated pillar columns for LC is presented. 2-D flow simulations are performed with a focus on electrokinetically driven flow, in order to evaluate the performance of the new method. The proposed foil shape is compared with geometrical shapes known from the literature, for various arrangements. It yields a much more uniform velocity field distribution and a decrease in plate height values up to 25%. In addition to shape optimization, a new method for spatial arrangement of structures is presented. With the aim of conserving the hydrodynamic balance, the axial spacing of the pillars is adjusted according to the proposed equivalent width approach. When compared with a fixed interpillar spacing in all directions, it increases the flow uniformity and results in an 18% lower plate height. A new direct simulation approach is implemented to model both flow field and retention for solid microfabricated pillar structures in the 2-D domain. This model, which defines retention as inward/outward fluxes through the wall surfaces as first order reactions, enables monitoring of the time-dependent process and an evaluation of the parameters affecting performance. The meaning of the obtained results in a practical setting, with limitations in photolithography and microfabrication, will be highlighted.