Airborne molecular contaminants (AMCs) have become a serious problem with recent advances in semiconductor manufacturing technology. The use of chemical filters to remove AMCs in cleanrooms is critical for improving the yield of semiconductor devices. The experimental FFU is designed for the evaluation of chemical filters. Silicon wafers exposed in the downstream air of chemical filters in the experimental FFU were investigated by Wafer Thermal Desorption—Gas Chromatography-Mass Spectrometry (WTD-GC-MS). Organic contaminants caused by outgassing from the chemical filter were detected on the surface of the silicon wafer and compared among various chemical filters. Results showed that the volatile organic compounds (VOCs) emitted from chemical filters adsorbed on the surface of silicon wafers located downstream of the filters. It was also found that the organic contamination on the surface was related to the amount of outgassing from the chemical filters. In addition, the rates of decrease of organic contamination emitted from various ULPA filters were compared using the experimental FFU. The rate of decrease of organic contamination emitted from the low-outgassing ULPA filter was also superior to that of the normal ULPA filter.