In this work, methods of design and fabrication of photonic bandgap structures (PBG) and photonic crystal waveguides based on SOI (silicon on insulator) are presented. In theory, a method that incorporates the plane wave expansion (PWE) method based on supercell with the finite-difference time-domain (FDTD) method with a perfectly matched layer (PML) boundary condition has been investigated. At first, PWE simulation will present a band structure. Then according to the band structure, FDTD tool can simulate a light propagation and can obtain optimized parameters easily. With the method, several photonic crystal devices suitable for 248nm Deep UV lithography and 0.18um ion-beam etching are designed and fabricated.