A method for planarizing a substrate surface having a non-planar surface topography comprises forming a material layer over the substrate, the material layer having a surface topography, determining the surface topography of the material layer, and forming a mask using information relating to the surface topography of the material layer. The mask defines portions of averaging regions of the material layer for selective removal to equalize the averaging regions in average height, the averaging regions having a maximum dimension. The material layer is etched using the mask, and a planarizing layer is formed over the substrate surface. The planarizing layer provides a low-pass lateral filtering effect characterized by a length greater than the maximum dimension of the averaging region. The mask is created by determining the localized height of the material layer across a surface and using the mask to etch away corresponding portions of the material layer so that the average surface of the material layer approximates a planar surface. The surface of the second material layer is substantially planar. The system and method for planarizing a material layer provides for forming a substantially planar layer of material over a non-planar topography.