A hp-finite element method is implemented to numerically study the modes of waveguides with two dimensional cross-section and to compute electromagnetic scattering from three dimensional objects. A method to control the chromatic dispersion properties of photonic crystal fibers using the selective hole filling technique is proposed. The method is based on a single hole-size fiber geometry, and uses an appropriate index-matching liquid to modify the effective size of the filled holes. The dependence of dispersion properties of the fiber on the design parameters such as the refractive index of the liquid, lattice constant and hole diameter are studied numerically. It is shown that very small dispersion values between 0±0.5ps/nm-km can be achieved over a bandwidth of 430-510nm in the communication wavelength region of 1300-1900nm. Three such designs are proposed with air hole diameters in the range 1.5-2.0μm. A novel multi-core fiber design strategy for obtaining a at in-phase supermode that optimizes utilization of the active medium inversion in the multiple cores is proposed. The spatially at supermode is achieved by engineering the fiber so that the total mutual coupling between neighboring active cores is equal. Different designs suitable for different fabrication processes such as stack-and-draw and drilling are proposed. An important improvement over previous methods is the design simplicity and better tolerance to perturbations. The optimal implementation of perfectly matched layer (PML) in terms of minimizing the computational overhead it introduces is studied. In one dimension it is shown that PML implementation with a single cell and a high order finite element produces minimal overhead. Estimates of optimal cell size and optimal finite element degree are given. Based on the single cell implementation of PML in three dimensions, field enhancement in metallic bowties is computed.