In this study, a novel method to fabricate highly aligned lamellar nanostructures in a millimeter-scale large area was demonstrated by directing the self-assembly of block copolymer (BCP) thin films with a temporary thickness-gradient micropattern via simple two-step thermal annealing. In the first step of thermal annealing, the BCP nanostructure is latently guided by a phenomenon known as "geometric anchoring" for the area with a thickness gradient. The second annealing step causes thermal reflow of the height gradient micropattern with a sufficiently large curvature to flatten the micropattern. The shear stress generated by thermal reflow enlarged the grain of the BCP nanostructure, resulting in a highly aligned lamellar pattern over the entire area. Finally, the formation of periodic nanopatterns in large area was ensured by performing grazing-incidence small-angle x-ray scattering. This innovative approach in directing the BCP self-assembly promotes the fabrication of highly aligned nanostructures in large areas through cost-effective and simple thermal imprinting method and designed two-step heat treatment.