Optical waveguide based on symmetric and asymmetric Mach-Zehnder interferometer(MZI) type was designed, fabricated and measured the optical characteristics for the application of biosensor. The wavelength of the input optical signal for the device was 1550 nm. And the difference of refractive index was $0.45;{Delta}\%$ between core and cladding of the device. The TM(Transverse Magnetic) mode optical properties of the biosensor were analyzed with the refractive index variation of gold thin film deposited for overclad. Nowadays, nano-photonic crystal structures have been paied much attention for its high optical sensitivity. There is a technique to realize the structure, which is called Dip-Pen Nanolithography(DPN) process. The process requires a nano-scale process patterning resolution and high reliability. In this paper, two dimensional nano-photonic crystal array on the surface was proposed for improving the sensitivity of optical biosensor. And the Dip-Pen Nanolithogrphy process was investigated to realize it.