Novel micro patterning techniques have been developed for the patterning of volatile functional materials which cannot be conducted by conventional photolithography. First, in order to create micro patterns of volatile materials (such as bio-molecules and organic materials), micro-contact printing and shadow mask methods are investigated. A novel micro-contact printing technique was developed to generate micro patterns of volatile materials with variable size and density. A PDMS (Polydimethylsiloxane) stamp with 2-dimensional pyramidal tip arrays has been fabricated by anisotropic silicon etching and PDMS molding. The variable size of patterns was achieved by different external pressures on the PDMS stamp. A novel inking process was developed to enhance the uniformity and repeatability in micro-contact printing. The variable density of patterns could be obtained by alignment using x-y transitional stage and multiple stamping with a z-directional moving part. Second, for direct patterning of small molecule organic materials (e.g. pentacene), a novel shadow mask method has been developed with a simple and accurate alignment system. To make accurate dimensions of patterning windows, a silicon wafer was used for the shadow mask since a conventional semiconductor process gives a great advantage for accurate and repeatable fabrication processes. A sphere ball alignment system was developed for the accurate alignment between the shadow mask and the silicon substrate. In this alignment system, four matching pyramidal cavities were fabricated on each side of the shadow mask and silicon wafer substrate using an anisotropic silicon bulk etching. By placing four steel spheres in between the matching cavities, the self-alignment system could be demonstrated with 2-3um alignment accuracy in x-y directions. For OTFT (Organic thin film transistor) application, an organic semiconducting layer was directly deposited and patterned on the substrate using the developed shadow mask method. On the other hand, novel embedding techniques were developed for enabling conventional semiconductor processes including photolithography to be applied on the small substrate. The polymer embedding method was developed to provide an extended processing area as well as easy handling of the small substrate. As an application, post CMOS (Complementary metal-oxide-semiconductor) integration of a relatively large microstructure which might be even larger than the substrate was demonstrated on a VCO (Voltage-controlled oscillator) chip. In addition, micro patterning on the optical fiber was demonstrated by using a silicon wafer holder designed to surround and hold the optical fiber. The micro Fresnel lens could be successfully patterned and integrated on the optical fiber end.