To pattern thin polymer films via electrohydrodynamic instabilities, we design and utilize 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 that are prealigned 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 are also produced mainly due to the dynamic merging among preformed pillars. Finally, we find vertex symmetry of the mask pattern is necessary for generating and preserving ordered patterns on the polymer film.