Scattering by an isolated defect embedded in a dielectric medium of two-dimensional periodicity is of interest in many sub-fields of electrodynamics. Present approaches to compute this scattering rely on either the Born approximation and its quasi-analytic extensions or ab initio computation that requires large domain sizes to reduce the effects of boundary conditions. The Born approximation and its extensions are limited in scope, while the ab initio approach suffers from its high numerical cost. In this paper, I introduce a hybrid scheme in which an effective local electric susceptibility tensor of a defect is estimated by solving an inverse problem efficiently. The estimated tensor is embedded into an S-matrix formula based on the reciprocity theorem. With this embedding, the computation of the S-matrix of the defect requires field solutions only in the unit cell of the background. In practice, this scheme reduces the computational cost by almost two orders of magnitude, while sacrificing little in accuracy. The scheme demonstrates that statistical estimation can capture sufficient information from cheap calculations to compute quantities in the far field. I outline the fundamental theory and algorithms to carry out the computations in high dielectric contrast materials, including metals. I demonstrate the capabilities of this approach with examples from optical inspection of nano-electronic circuitry where the Born approximation fails and the existing methods for its extension are also inapplicable.