The polymer melt confined within two planner electrodes can self assemble into ordered micro-structures under the influence of an electric field. A significant challenge to the implementation of this “bottom up” approach to patterning surfaces via self assembly induced by the electrohydrodynamic (EHD) instabilities is the natural tendency to form multidomain structures. We designed and utilized two different kinds of mask patterns to guide pillars into alignment over regions much greater in extent than their natural domain sizes. First, narrow protruding ridges that intersect to form regular patterns on the mask trigger the growth of pillars beneath. Later, square and triangular packings of pillars develop in the regions enclosed by those ridges, preserving the registry from one domain to the next over a much larger area than within individual domains in unpatterned portions of the mask. Second, small square protrusions pre-aligned into a large regular array on the mask guide the formation of square packings of pillars in domains that conform to the mask, forming a large array of pillars. Novel structures involving a combination of linear ridges and pillars were also produced mainly due to the dynamic merging among pre-formed pillars. We also found vertex symmetry of the pattern on the mask is necessary for generating and preserving ordered patterns on the polymer film. Finally, we will briefly discuss the mechanisms for formation of several hierarchical patterns we observed recently. This first step in enabling engineering of electrohydrodynamic patterning over large areas opens the path towards applications requiring larger areas of well-arrayed patterning.