The layer-by-layer (LBL) assembly of poly(diallyldimethylammonium chloride) and poly(sodium styrene sulfonate) on poly(sulfo propyl methacrylate) brushes resulted in films with nanometer- and micrometer-sized holes and ledges, observed by atomic force microscopy and scanning electron microscopy. Polyelectrolyte assembly was followed by the quartz microbalance technique. The formation of ledges and holes is explained by the interaction of the brush polymers with the incoming polyelectrolytes during the LBL assembly, inducing a spatially localized and self-organized accumulation of the assembled polymers.