Abstract: Micro scale 3D complex structures are critical for the performance of Microelectromechanical Systems, micro-fluidic systems, photonic crystals, and meta-materials. It still remains a challenge for traditional silicon micro-fabrication technique. Here we developed a projection micro-stereolithography system which is capable of machining arbitrary 3D shapes in micrometer scale, in a layer by layer scheme. The key component of our system is a dynamic mask which can generate arbitrary pattern according to the computer code. Using a projection lens, the mask pattern is focused on the light curable resin and forms layers of a 3D structure. We also investigated the gray scale exposure using the dynamic mask, which enabling us to fabricate smooth structures. A sublimation apparatus was developed to solve the stiction problem and increase the reliability and yield. We applied this fabrication method in making a metamaterial THz filter, as well as artificial micro-circulation systems for tissue engineering purpose. The later part of the thesis is devoted in the investigation of the single molecular machines ([2]Rotaxane). We demonstrate the evidence of electrochemically switching of the ring in [2]Rotaxane molecules. We characterized the life time of the ring metastable state and the energy barrier for the ring to move. Follow this finding, we studied nano-patterning of [2]Rotaxane SAM layer using conductive AFM.