We report new methods of surface modifications for confining and aligning biological macromolecules and liquid crystals on microstructured surfaces. Microcontact printing and polyelectrolyte adsorption were used to pattern and control surface properties of silicon microchannels fabricated by photolithography and etching. We show that the wettability inside and on top of the microstructures can be independently varied by selective deposition of a hydrophobic monolayer using microcontact printing, whereas the surface charge, reactivity, and bio compatibility in the microchannels can be adjusted by adsorbing polyelectrolytes to the surface. A near ideal contrast in surface properties was achieved by microcontact printing on preadsorbed polyelectrolyte layers. Three-dimensional laser scanning confocal microscopy was used to characterize the wetting behavior of biological macromolecules (lipids, DNA, microtubules) confined in the microstructures. DNA molecules in concentrated solutions were observed to orient along the microchannels, as a result of surface confinement, when their contour length approached the width of the microchannels. We demonstrate that the surface microstructures may be used to control the mesoscopic defect structures and defect sizes of liquid crystals by studying the defect structure of 8CB (4 ' -n-octyl-4-eyanobiphenyl) as a function of the widths and depths of the microchannels. The order induced due to microchannel confinement of biological molecules has the potential of resulting in unique structure characterization of highly oriented biological macromolecules using synchrotron X-ray microdiffraction methods.