During the mean surface residence time measurements by means of molecular beam relaxation method it is often found that an error starts to appear as the mean residence time becomes comparable to the molecular beam modulation period. An analysis has been made to clarify that this is due to a systematic error which occurs during data processing using Fast Fourier Transform software. Fourier transform is usually performed in a single period of the desorbed molecular beam time-of-flight signal, while the resultant signal is a sum of the signals at present period and those initiated in the past periods. This signal overlapping creates a systematic error especially at high frequency components of Fourier transform.