Microfibers are important components in the construction of fiber reinforced materials; however, precisely picking, placing and orienting microfibers remains a difficult task. This paper introduces a capillary manipulation method for handling microfibers. The micromanipulation method combines a capillary pick-and-place technique and super hydrophilic - super hydrophobic patterned surfaces. Capillary pick-and-place method was used to transfer the fibers to the substrate, and the patterned super hydrophilic – super hydrophobic surfaces was used for alignment of the microfibers. We studied influences of the key parameters including the wetting properties of the substrate, the volume of the droplet and the size of the super hydrophilic – super hydrophobic patterns on the capillary micromanipulation of microfibers. The proposed method has great potential for manufacturing complex microstructures out of microfibers.