The absorption of z-cut quartz windows in the terahertz region of interest is very low, with an extinction coefficient of approximately zero and the real part of the refractive index being approximately constant. Inserting windows into the beam path mostly lead to a longer time delay before detecting the pulse on the order of 20 ps for a window thickness of 3 mm. This could be utilised when calculating the absorption coefficient. While the spectral shape of the absorption was not influenced by the reference thickness, the absolute values were. By shifting the acquired reference waveform by about 20 ps and subsequently using the method of Duvillaret et al., the absorption coefficient was calculated. The absolute shift necessary depended on the thickness of the windows and sample. By comparing the absorption coefficient of pure water with literature values, introducing a time delay of 18.43 ps to the reference data recovered the absorption. This is illustrated in Figure and. Due to the optical design of the Terapulse 4000 instrument, a small feature was visible in the reference waveform at a time-delay of approximately 15 ps following the main peak. This introduced artefacts in the frequency domain unless temporal windowing was applied. The reference waveform was therefore zero-padded to remove those artefacts and Figure shows both the reference and sample waveforms that were being used to calculate the absorption coefficient. Application of a Fourier transformation resulted in the power spectra shown in Figure .