Previously published FFT dose calculations and their verifications have been performed for field sizes greater than 10 cm x 10 cm with photon energies up to 18 MV [Zhu and Boyer, Phys. Med. Biol. 35, 351-368 (1990)]. With a smaller field size at megavoltage energies, lateral electronic disequilibrium exists in low density inhomogeneities which is not handled properly by the FFT calculations. In this paper, we extend FFT dose calculations to address this problem without significantly increasing the computational time. We employ lateral scaling of the field size at each depth along with an inverse scaling of the resultant dose distribution. The concept of effective density in introduced for the lateral and inverse scaling. We demonstrate that electron transport can be adequately captured in the presence of inhomogeneities, thus improving 3D FFT dose calculations in inhomogeneous media.