Manipulation of long chain DNA at the level of single molecules is of great interest to biotechnology and nanotechnology. We have used various types of micro/nanostructures to uncoil, trap, align, and immobilize DNA molecules in liquid flows and at an air-water interface. We observed that DNA molecules were trapped by micropillars longer in electrokinetically driven flow than in capillary-driven flow. Brownian dynamics simulation using bead-spring chain model is conducted. It indicates a possible contribution of friction force between DNA and the micropillars to this phenomenon. We have also stretched DNA molecules and patterned them into well-defined arrays on a polydimethylsiloxane (PDMS) surface with topological micro/nanostructures through a dewetting method. Arrays of stretched DNA molecules with well-defined locations, orientations, and lengths are generated on a surface with microwells and the dewetting process is simulated by a finite volume discretization approach featured by simulating a moving free surface. Arrays of long DNA nanowires are also produced on micropillars by a similar dewetting mechanism. This technique has been extended to nanopillars with a sub-100 nm gap, providing a novel tool not only for fundamental study of nanoscale fluidic mechanics and single DNA dynamics but also for nanofabrication. We are converting the nanowire-micro/nanopillar arrays into nanochannel-micro/nanowell arrays for the study of dynamics of small DNA and RNA molecules in confined environment for bioseparation.