Polymer nanocomposites are composed of polymer materials reinforced with nano fillers. In the present study the effective thermal conductivity of the composites filled with nanofillers has been investigated using commercially available finite element software ABAQUS 6.11. The nanofillers used were alumina particles and multi-walled carbon nanotubes (MWNTs) and the matrix was considered to be made of epoxy. For the analysis 2D and 3D Representative Volume Elements (RVEs) were generated using Random Sequential Adsorption (RSA) algorithm using MATLAB and Python scripts. Thermal conductivity was found out for 2D and 3D RVEs for different area and weight fractions respectively. Two different shapes of the alumina nanoparticles were considered: spherical (circular) and ellipsoidal (elliptical) for 3D (2D) analysis. It was found that the thermal conductivity was increased with the addition of nanofillers. The increase in thermal conductivity was approximately same for both types of inclusions at corresponding area or weight fractions in 2D or 3D analysis. The results showed that addition of MWNTs to the composites lead to a significant increase in thermal conductivity than spherical or ellipsoidal inclusions.