Spectral methods using Fast Fourier Transform (FFT) algorithms have recently seen a surge in interest in the mechanics community. The present contribution addresses the critical question of determining local mechanical fields using the FFT method in the presence of interfacial defects. Precisely, the present work introduces a numerical approach based on intrinsic discrete Fourier transforms for the simultaneous treatment of material discontinuities arising from the presence of disclinations, i.e., rotational discontinuities, and inhomogeneities. A centered finite difference scheme for differential rules are first used for numerically solving the Poisson-type equations in the Fourier space to get the incompatible elastic fields due to disclinations and dislocations. Second, centered finite differences on a rotated grid are chosen for the computation of the modified Fourier-Green's operator in the Lippmann-Schwinger-Dyson type equation for heterogeneous media. Elastic fields of disclination dipole distributions interacting with inhomogeneities of varying stiffnesses, grain boundaries seen as DSUM (Disclina-tion Structural Unit Model), grain boundary disconnection defects and phase boundary "terraces" in anisotropic bi-materials are numerically computed as applications of the method.