A nano filter showing the Knudsen flow was demonstrated by a modification of a membrane constructed from rice husk silica. The membrane was prepared by pressing and sintering micron sized rice husk silica with 4 nm pores. The membrane showed a permeability of 5.2 × 10−8 mol m−1 sec−1 Pa−1 for H2 and ratios of gas permeability 2.1 and 3.2 for k(H2)/k(CH4) and k(H2)/k(CO2), respectively. When the membrane was treated by filtration of ∼100 nm sized rice husk silica particles, the permeability decreased to 4.9 × 10−8 mol m−1 sec−1 Pa−1 and the ratios increased to 2.2 and 3.4. In the case of the membrane after treatments with the dispersion and chemical deposition of tetraethylorthosilicate (TEOS), the corresponding permeability and ratios of the membrane were 1.8 × 10−8 mol m−1 sec−1 Pa−1, and 2.9 and 4.5, respectively. From the change of the ratio of gas permeability for the membrane with modifications, it is suggested that ∼100 nm sized rice husk silica particles pack the large pores among the micron sized rice husk silica particles while the chemical deposition of tetraethylorthosilicate (TEOS) reveals the gas flow through 4 nm pores in the rice husk silica by blocking large pores.