A novel method to predict the macroscopic effective thermal conductivity of filled composites, based on its microstructural characteristics is developed and validated. A finite element method which incorporates the effect of microstructural characteristics such as filler aspect ratio, interfacial thermal resistance, volume fraction, and filler and fiber dispersion to determine the effective thermal conductivity of a composite with circular and rectangular fillers is presented. Filler interactions and chain formation effects are included in the model. To overcome the laborious task of repeated finite element model generation, an algorithm which generates the positions and orientations of the fillers in the matrix is developed. The automated model development capability is used to create several microstructures for finite element analysis. The trends predicted by the finite element models are compared with existing analytical models and available experimental results. The advantage of this method over existing analytical and semi-empirical models is that it can handle interactive effects, provide a detail heat flux pattern, and also model high filler volume fractions.