Based on the fact that SiO(2) can dissolve in HF solution, three kinds of diatom frustules were treated with 1% HF solution at room temperature. Given the proper reaction times (0-2 h for the diatoms Coscinodiscus and Navicula, and 0-3 h for the diatom Melosira), the size of the pores on the frustules gradually increased and the structures of the frustules remained. While HF treatment does not affect the composition, chemical bonds, or photoluminescence signature of the diatom frustules, the treatment reduces their surface areas. This method may be beneficial to diatom studies, diatom nanotechnology, and diatom device applications that make use of diatom pores.