Soft lithography techniques have become leading mesoscale approaches for replicating topographic features in polymer films. So far, the modified polymer films formed by soft lithography only featured topographic heterogeneity. Here we demonstrate the application of soft lithography techniques to block copolymer films, and show that the preferential affinity of one of the blocks to the stamping material leads to chemical heterogeneity that corresponds to the topographic features. Detailed surface and structural characterization of the patterned films provided information on its three-dimensional structure, revealing insights on the domain reorganization that takes place in the block copolymer film concomitantly with topography formation. The formed structures were utilized for selective assembly of gold nanoparticles into hierarchical structures. The versatility of this combined nanofabrication/self-assembly approach was demonstrated by the assembly of two types of metallic nanoparticles into two different arrangements with full control over the location of each type of nanoparticles.