A block copolymer-based assembly approach for the creation of nano-patterned polyelectrolyte multilayers over cm2-scale areas is presented. Up to 5 bi-layers were selectively assembled on top of specific nano-domains featuring different morphologies. The successful isolation of nanoscale objects corresponding in shape to the template features is also demonstrated. This methodology is applicable to different types of polyelectrolytes, and opens up a new dimension for layer-by-layer construction.