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Biofilms are thin layers of microorganisms in which cells adhere to each other and stick to a surface. They are resistant to antibiotics and disinfectants due to the protection from extracellular polymeric substance (EPS), which is a gel like self-produced matrix, consists of polysaccharide, proteins and nucleic acids. Biofilms play significant roles in many applications. In this document, we provide analysis about effects and influences of biofilms in microfiltration and dental plaque removing process. Differential equations are used for modelling the microfiltration process and the optimal control method is applied to analyze the efficiency of the filtration. The multiphase fluid system is introduced to describe the dental plaque removing process and results are obtained by numerical schemes.