Film thickness, free carrier concentration and free carrier mobility are critical figures of merit for silicon carbide epitaxial growth. Room temperature Fourier Transform Infrared (FTIR) reflection spectroscopy can estimate these parameters non-destructively and is capable of high-resolution wafer mapping. Commercially available equipment has greatly simplified the application of this technique by coupling a high performance automated spectrometer with model-based data analysis and interpretation based on the personal computer. While powerful numerical techniques run fast and efficient on modern computers, it is essential that low-order, well-conditioned models are needed. The observed reflectance spectrum is the result of reflection and refraction of light at different interfaces due to constructive and destructive interference. The estimation of film thickness and free carrier concentration for single epitaxial layers has been improved by studying the Longitudinal Optical Phonon Plasmon (LPP) coupled modes. However, the addition of multiple layers introduces many degrees of freedom, which complicates parameter extraction. The multiple epitaxial layer stacks studied were intended for Metal Semiconductor Field Effect Transistor (MESFET?s) on both conducting and semi-insulating substrates. The thickness estimation of the n-channel in the MESFET stack on semi-insulating substrate is improved by preconditioning the curve fit for plasma frequency obtained from doping estimation from capacitance voltage profiling or by observing an LPP- peak.