Conductive polymers are a class of materials with vast potential for tomorrow's ultra-large-scale technologies as they combine structural and functional diversity with flexible synthesis and processing approaches. A missing component, with their subtle chemical structure, is reliable building at nanoscale. Here we report on the patterning of polyaniline, a prototypical conjugated polymer, with an unprecedented areal patterning order and density exceeding 0.25 teradot/inch(2). With template-confined growth, through platinum-surface-catalyzed polymerization of aniline, highly ordered arrays of distinct polyaniline nanowires are produced with a typical diameter <or=15 nm and aspect ratio higher than 20. Up-scaling is straightforward. Complex three-dimensional structural control is achieved through a direct pattern transfer via resist- and dose-modulated electron beam lithography. The morphology-modulated nanowires self-assemble in key-lock type architectures induced by the structure asymmetry and nonuniformity of the capillary forces associated with the re-entrant features.