A system for recording transmission spectra of a sample with a spectrometer that produces baseline-free molecular response signal. A method for producing baseline-free signals includes applying a logarithmic function to a measured transmission spectrum to form an intermediate spectrum. Applying an inverse Fourier transform to the intermediate spectrum generates a modified free-induction-decay (m-FID) signal, which allows for the separation of molecular absorption features from baseline effects present in the m-FID signal. A weighting function is then applied that suppresses temporal portions of the m-FID signal that correspond to sources of baseline fluctuations as well as periodic effects (e.g. etalons). The method generates a baseline-suppressed m-FID signal that is converted to an absorption spectrum, which exhibits suppressed contributions from baseline fluctuations and periodic effects. When this method is combined with a spectral fitting model it generates measurements of physical properties of the sample without requiring correction for the light source intensity.