A filtration-aided acid cleaning method was used to collect biosilica structures from a diatom culture medium, natural seawater, or water bloom. Cell extraction, acid cleaning, and acid removal were all performed on a polytetrafluoroethylene (PTFE) filter cloth, significantly improving the treatment capacity and efficiency of the traditional acid wash method. Five typical diatoms were cultivated in the laboratory for acid cleaning. Different growth speeds were introduced, and different process parameters for acid cleaning were utilized. After the acid cleaning, biosilica structures were collected from the frustules of diatoms using different methods. Girdle bands and valves of Coscinodiscus sp. were separated by floating of the valves. Central spines of Ditylum brightwellii and valves of Skeletonema costatum were separately collected by settling or filtration. Rod-like frustules, such as those of Bacillaris paradoxa, are not suitable for large quantities of acid wash. The silica structures were observed and tested using an AFM-calibrated glass needle to determine their elasticity. Elasticity tests showed that ringent girdle bands are more flexible than complete ones (Coscinodiscus sp.) and that both long-chain clusters of Nitzschia palea and central spines of D. brightwellii have certain elasticities. The required pressure for deforming or breaking the biosilica structures of diatoms was also determined.