Nanostructured materials have shown great potential in improving the sensitivity and reliability of chemical and biological sensors. The ability to control the geometric shape (size, separation, orientation, alignment, etc.) of nanostructures and to integrate nanostructures from different materials becomes one of the great challenges for sensor fabrication. Glancing angle deposition techniques can fabricate well-aligned three-dimensional nanostructures through computer programming. By rotating the substrate in both polar and azimuthal directions, one can fabricate desired nanostructures, such as nanorod arrays with different shapes, nanospring arrays, and even multilayer nanostructures. This method offers full three-dimensional control of the nano-structure with the additional capability of self-alignment and can be easily integrated into microdevices and optical devices. With the high surface area and high aspect ratio of those nanostructures, different sensors such as enzyme-based biosensors and optical sensors with higher sensitivity have been demonstrated.