The procedures used to estimate structural modal parameters as natural frequency, damping ratios, and mode shapes are generally based on frequency methods. However, methods of time-frequency analysis are highly sensible to the parameters used to calculate the discrete Fourier transform: windowing, resolution, and preprocessing. Thus, the uncertainty of the modal parameters is increased if a proper parameter selection is not considered. In this work, the influence of three different time domain windows functions (Hanning, flat-top, and rectangular) used to estimate modal parameters are discussed in the framework of ISO 18431 standard. Experimental results are conducted over an AISI 1020 steel plate, which is excited by means of a hammer element. Vibration response is acquired by using acceleration records according to the ISO 7626-5 reference guides. The results are compared with a theoretical method and it is obtained that the flat-top window is the best function for experimental modal analysis.