This paper describes an all-soft, templated assembly of block copolymers (BCPs) with programmable alignment. Using polymeric nanowrinkles as a confining scaffold, poly(styrene)-block-poly(dimethylsiloxane) (PS-b-PDMS) BCPs were assembled to be parallel or perpendicular to the wrinkle orientation by manipulating the substrate strain. Self-consistent field theory modeling revealed that wrinkle curvature and surface affinity govern the BCP structural formation. Furthermore, control of BCP alignment was demonstrated for complex wrinkle geometries, various copolymer molecular weights, and functional wrinkle skin layers. This integration of BCP patterning with flexible 3D architectures offers a promising nanolithography approach for next-generation soft electronics.