A spectroscopy system and method in which the optical path following the interferometer includes a Jacquinot stop having an aperture disposed substantially at its focal point. The Jacquinot stop includes a reflective surface substantially non-orthogonal to the longitudinal axis of the path and facing the source of the IR signal containing an interferogram. The aperture passes an inner portion of the incident IR signal, while the reflective surface reflects an outer portion. The reflected outer portion of the incident IR signal, which contains erroneous spectral information due to inherent flaws in the interferometer optics, is thereby effectively removed from the original incident IR signal ultimately used to irradiate the sample, and yet still be made available for use in monitoring background spectra of the sampling optics.