Microfibers are important components in the fabrication of fiber-reinforced materials, and the distribution and alignment of microfibers can affect the mechanical, electrical, and thermal properties of the fiber-reinforced materials. However, it remains a challenge to precisely align and distribute microfibers on a large scale at a high throughput. This paper reports a facile droplet-directed method to transport and self-align microfibers to micro trenches using droplets ejected from a non-contact dispenser. Employing super hydrophilic-super hydrophobic trenches with sizes matching the microfibers, the method can align and transport randomly dispersed fibers around trenches into the trenches as desired. We studied this alignment and transport mechanism and the results suggest that liquid volume is critical to allow the capillary force to be dominant leading to the success of the process. We demonstrated that microfibers having an aspect ratio of 200, a diameter of 15 μm and a length of 3 mm, canreliably self-align to super hydrophilic-super hydrophobic trenches and transport to the target location, achieving linear alignment accuracy of 0.5 μm and angular accuracy of 0.1°. The high accuracy and fast process of the proposed technique may greatly impact larger scale and high throughput construction of complex microstructures using microfibers.