In an early work we have demonstrated the possibility of using Monte Carlo generated pencil beams for 3D electron beam dose calculations. However, in this model the electron beam was considered as monoenergetic and the effects of the energy spectrum were taken into account by correction factors, derived from measuring central-axis depth dose curves. In the present model, the electron beam is considered as polyenergetic and the pencil beam distribution of a clinical electron beam, of a given nominal energy, is represented as a linear combination of Monte Carlo monoenergetic pencil beams. The coefficients of the linear combination describe the energy spectrum of the clinical electron beam, and are chosen to provide the best-fit between the calculated and measured central axis depth dose, in water. The energy spectrum is determined by the constrained least square method. The angular distribution of the clinical electron beam is determined by in-air penumbra measurements. The predictions of this algorithm agree very well with the measurements in the region near the surface, and the discrepancies between the measured and calculated dose distributions, behind 3D heterogeneities, are reduced to less than 10%. We have demonstrated a new algorithm for 3D electron beam dose calculations, which takes into account the energy spectra. Results indicate that the use of this algorithm leads to a better modeling of dose distributions downstream, from complex heterogeneities.