Accurate knowledge of ellipsometric parameters of material surfaces is important for determination of optical properties of bare surfaces, thickness and refractive index of thin films and for study of transport phenomena in ultra-thin films. In this study an analytical framework, in the context of Fourier coefficients, is presented that allows window birefringence to be incorporated in the analysis of ellipsometric measurements. The method is applied to analysis of data obtained on an amorphous carbon sample in the wavelength range 400-700 nm at temperature 25 degrees C. It is demonstrated that the inferred refractive indices of the sample may be in error by 28% or more when birefringence effects are not included in the analysis. Thus, when ellipsometry is to be used for inference of refractive indices, film thickness and/or transport properties of thin films deposited on solid surfaces, window birefringence effects may not be neglected.