Ellipsometry measures the relative intensity of and the phase difference between the parallel and perpendicular components of a polarized electric field vector interacting with a sample. In this paper, a technique using polarized Fourier transform infrared spectroscopy for measuring this information,as the complex optical density function, is presented. The advantage of the complex optical density function is that it, relates the properties of the polarized electric field vector to the supporting surface instead of the plane of incidence. In this configuration, the precise positioning of the sample surface compared to the reference surface and the reproducibility of the analyzer movement are the most important contributions to the errors in the complex optical density function. We demonstrate that these errors are small compared to the complex optical density function measured from the presence of an organic monolayer on a metal surface. The measured complex optical density function provides a signature that is related to both the thickness and molecular structure of the sample layers. Electromagnetic wave theory can be used to predict the signature for any set of sample properties. By matching measurement and prediction, the thicknesses and molecular structures of a series of alkanethiol monolayers are determined.