Ultra-fine (<1 microm) microfilters are required to effectively trap microbial cells. We designed microfilters featuring a rain drop bypass architecture, which significantly reduces the likelihood of clogging at the cost of limited cell loss. The new rain drop bypass architecture configuration has a substantially lower pressure drop and allows a better efficiency in trapping protozoan cells (Cryptosporidium parvum and Giardia lamblia) in comparison to our previous generation of a microfilter device. A modified version displaying sub-micron filter gaps was adapted to trap and detect bacterial cells (Escherichia coli), through a method of cells labeling, which aims to amplify the fluorescence signal emission and therefore the sensitivity of detection.