1. A fluorescence molecular tomography imaging system comprising: an excitation light source; an optical imaging apparatus configured to direct light from the excitation light source into a subject at a plurality of locations; a detector configured to detect at multiple locations fluorescent light emanating from a region of the subject; and a memory having instructions stored thereon, wherein the instructions, when executed by a processor, cause the processor to: using data corresponding to the detected fluorescent light, establish a forward model of (a) excitation light propagation from the excitation light source to the region of the subject and of (b) fluorescent light propagation from the region of the subject to the detector, such that light propagation is modeled as if there is no discontinuity in refraction index at a surface of the subject, wherein one or more virtual-matching transformations are applied to the data corresponding to the detected fluorescent light to account for a refractive index discontinuity at the surface of the subject, wherein application of the one or more virtual-matching transformations to the data corresponding to the detected fluorescent light results in transformed data, wherein each of the one or more virtual-matching transformations is derived from a boundary condition which relates measured flux to surface-dependent average intensity and expresses average intensity that would be present in absence of the surface; and obtain a tomographic representation of the region of the subject using the forward model in combination with the transformed data.