We report a new type of cylindrical-shaped micropillar array in a microfluidic device to enhance the dispersion of cell clusters and to isolate individual cells into individual micro-hydrogels. The installed micropillars act as a sieve for the breaking of Escherichia coli (E. coli) clusters into single cells in a polymer mixture. This proposed strategy and device would be a useful platform for genetically modified microorganisms for practical applications.