A chemical pattern layer including an orientation control material and a prepattern material is formed over a substrate. The chemical pattern layer includes alignment-conferring features and additional masking features. A self-assembling material is applied and self-aligned over the chemical pattern layer. The polymeric block components align to the alignment-conferring features, while the alignment is not altered by the additional masking features. A first polymeric block component is removed selective to a second polymeric block component by an etch to form second polymeric block component portions having a pattern. A composite pattern of the pattern of an etch-resistant material within the chemical pattern layer and the pattern of the second polymeric block component portions can be transferred into underlying material layers employing at least another etch.