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We have developed a new algorithm for electromagnetic inverse scattering problems in inhomogeneous media using finite-difference frequency-domain (FDFD) forward modeling, referred to as the FDFD-based inversion method. The key issue of this method is to build a linear expression for the inverse problem from an FDFD forward model by using Born approximation to neglect mutual coupling between scattered pixels and to then solve for the inverse coefficient matrix. An important advantage of this matrix-based method is that there is no need to specify a Green's function. As such, this inverse scattering algorithm is easily implemented and is robust to the heterogeneity in the background. We test the algorithm with a microwave subsurface object detection application using cross-well radar. The new method is compared with conventional inversion using Green's function-based Born approximation. Numerical experiments are presented for a 2-D borehole geometry for buried object detection in uniform soil and in multilayered soil backgrounds.