A method of controlling both alignment and registration (lateral position) of lamellae formed from self-assembly of block copolymers, the method comprising the steps of obtaining a substrate having an energetically neutral surface layer comprising a first topographic “phase pinning” pattern and a second topographic “guiding” pattern; obtaining a self-assembling di-block copolymer; coating the self-assembling di-block copolymer on the energetically neutral surface to obtain a coated substrate; and annealing the coated substrate to obtain micro-domains of the di-block copolymer.