Due to the low THz radiation energy and narrow pulse width(picosecond range), as a new spectral analysis method, terahertz time-domain spectroscopy(THz-TDS) technology is nondestructive and high-temporal-resolution when being used to extract optical parameters of samples. Fabry-Pérot interference is a crucial obstacle in extracting optical parameters of thin wafers in the THz-TDS through-transmission mode. A reliable algorithm was proposed and tested to simultaneously filter Fabry-Pérot interference and obtain precise optical characterization of thin wafers. The algorithm employs a band-stop filter immediately and exclusively designed for every single sample to the initial refractive index and absorption coefficient. Experimental results of doped silicon wafers and amino acid tablets confirming the utility of the algorithm were also presented.