Photonic crystal structures have been received considerable attention due to their high optical sensitivity. One of the techniques to construct their structure is the dip-pen lithography (DPN) process, which requires a nano-scale resolution and high reliability. In this paper, we propose a two dimensional photonic crystal array to improve the sensitivity of optical biosensor and DPN process to realize it. As a result of DPN patterning test, we have observed that the diffusion coefficient of the mercaptohexadecanoic acid (MHA) molecule ink in octanol is much larger than that in acetonitrile. In addition, we have designed and fabricated optical waveguides based on the mach-zehnder interferometer (MZI) for application to biosensors. The waveguides were optimized at a wavelength of 1550 nm and fabricated according to the design rule of 0.45 delta%, which is the difference of refractive index between the core and clad. The MZI optical waveguides were measured of the optical characteristics for the application of biosensor.