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This paper reports on a study to advance understanding of the microscale processes resulting in biological fouling of separation membranes operated on municipal secondary effluent. A primary goal was to explore the microscopic architecture of membrane biofilms using deconvolution fluorescence microscopy (DCFM)/3D recontruction to identify special features that might lead to novel or alternative chemical treatment strategies. Another goal was to use DCFM to identify and evaluate chemical agents that disrupt membrane biofilm structure. A microscope flow cell (MFC) was developed for this project which permitted qualitative and quantitative observations of initial bacterial attachment and early biofilm formation on dense cellulose acetate (CA-coated coverglasses).