Methods and systems for performing high throughput spectroscopic measurements of semiconductor structures at mid-infrared wavelengths are presented herein. A Fourier Transform Infrared (FTIR) spectrometer includes one or more measurement channels spanning a wavelength range between 2.5 micrometers and 12 micrometers. The FTIR spectrometer measures a target at multiple different angles of incidence, azimuth angles, different wavelength ranges, different polarization states, or any combination thereof. In some embodiments, illumination light is provided by a laser sustained plasma (LSP) light source to achieve high brightness and small illumination spot size. In some embodiments, FTIR measurements are performed off-axis from the direction normal to the surface of the wafer. In some embodiments, a Stirling cooler extracts heat from the detector of an FTIR spectrometer. In another aspect, measurements performed by one or more spectrometer measurement channels are combined with measurements performed by a mid-infrared FTIR spectrometer channel to characterize high aspect ratio structures.