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A procedure for incorporating inhomogeneous anisotropic variations in the refractive index tensor into two-dimensional finite element calculations of the guided mode characteristics of photonic crystal rods is presented. The stress tensor distribution is assumed to be known. Photonic crystal rod designs incorporating stress applying parts are analyzed using this procedure. The predicted guided mode structure is compared to the simplified case described by uniform birefringence revealing differences in the effective indexes of the guided modes, the effective area and eccentricity of the fundamental mode, the modal birefringence, and the overlap with the gain region of active devices. The method is applicable to all dielectric waveguide structures.