Among the many challenges facing the development of a molecular-based nanotechnology, the directed assembly of discrete molecular objects, and their controlled integration into macroscopic structures, is fundamental. The selective self-assembly or self-organizing characteristic inherent to certain molecules, for example DNA, is a property that could be exploited to address these challenges. This integration problem can be separated into more fundamental tasks: attaching molecular anchors to the macroscopic structures with high spatial resolution; assembling the discrete molecular objects; and positioning and attaching the molecular objects onto the macroscopic structures.Here, several aspects of these tasks will be discussed, for example using short DNA molecules as molecular anchors and their attachment to electrodes separated by a few ten nanometers; the generation of branched DNA complexes by molecular self-organization; and using AC electric fields for the manipulation, orientation, and positioning of DNA molecules.