In recent decades, there has been a significant evolution of microelectronic and semiconductor technologies towards the nanoscale. Both bottom-up and top-down integration concepts of functional nanostructures and nanoparticles into micro- and nanofabricated electronic components have become critical issues that decisively affect the performance of smart electronic systems in various application areas such as environmental sensing and energy harvesting.Functional nanostructures and nanoparticles of different shapes, sizes, morphologies, and materials are now used in various technical and industrial applications, medicine, pharmacy, biology, electronics, power engineering, ecology, and many other fields. However, the complex engineering challenge here is the integration of functional nanostructures, such as molecular components (e.g., functional self-assembled molecular monolayers or entities of desoxyribonucleic acid, DNA), organic or inorganic nanoparticles (metal, semiconductor, colloidal materials), or similar building blocks into nanolithographically fabricated environments.Manufacturing paradigms for this integration go beyond current CMOS- and MEMS-fabrication schemes. Scale-bridging and hybrid manufacturing schemes that combine established top-down manufacturing techniques for microelectronic devices, including aspects of nanotechnology, with bottom-up nanoassembly of molecules on unstructured and pre-structured substrates are required. Microsystems technology based on the combination of conventional semiconductor processing with biotechnological approaches has thus become an emerging field with manifold applications, especially in the field of sensor technology.This contribution describes two illustrative and innovative research questions in nanopatterning and system integration at the micro-nano-interface to motivate applications with new and unprecedented functionalities. The first research question focuses on network-based biocomputing (NBC) using biological agents driven by biomolecular motor proteins in a lithographically fabricated nanofluidic channel system. This approach opens up opportunities for energy-efficient solutions to complex mathematical problems as they make their way through the NBC network. Methods are required to create switchable and rewritable nano-networks to address different mathematical problems using a single NBC-chip. Therefore, stimuli-responsive materials must be selectively and locally deposited into the nano-network to control the transport of the filaments through the network.The second research question focuses on nanophotonic devices based on DNA origami. The high-precision arrangement of nanoscopic substructures using specific binding sites (capture ends) of the DNA origami enables the precise arrangement of DNA origami functionalized with individualized metal nanoparticles. This arrangement could be used to exploit individual spectral response mediated by plasmonic effects.From a technological perspective, top-down lithographic nanostructuring technologies and bottom-up nanostructuring technologies are the basis for new device concepts. The adaptability of nanostructures to the world of biological molecules and other nanoscopic building blocks such as quantum dots and nanoparticles enables novel, even personalized, devices and engineering solutions.