THz Time-Domain Spectrometry (TDS) probes the complex polarization response of materials. Various analytical procedures are applied by many to extract the associated material optical constants. This has commonly been done by iteratively varying material parameters in order to achieve a match between experiment and a theoretical transfer function (TF). Different ways of representing of multiple reflections inside the sample (a Fabry-Perot-like effect) are compared and their contribution to the uncertainty of material parameters is analysed. In addition, this paper offers a basis for data comparison between different THz-TDS systems in transmission mode. Finally, a clear distinction is made between a commonly used basic analysis and an enhanced one, in terms of associated uncertainties in determination of the real and imaginary parts of the complex refractive index.