Characterization of the structure of spatial inhomogeneities embedded in a highly scattering medium is required in many fields. In this paper, a model of a stratified medium embedded with an inhomogeneous ball is considered. With an assumption that the ball is small enough, a perturbation solution to diffusion equation is obtained with some boundary treatments. According to the characteristics of this solution in the two-dimensional Fourier space, a new weighted Fourier transform is used to process the surface data. After this process, a singularity appears at the center of the ball. Combining with the symmetry of the surface data, the information of three-dimensional position of the ball is determined.