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We report a facile, low-cost, and high-yielding microfluidic technology for in situ generating and arraying water-in-oil droplets by shrinking them to the order of femtolitres (fLs) as scalable batch micro-reactors. Instead of generating ultra-small droplets by the direct atomization, which requires dedicate control and high energy input, we shrink droplets to stable smaller ones by utilizing the controlled water diffusion in oil. This “shrunk to fL” method is combined with a three-dimensional microwell design to create high-density addressable droplet arrays. As the result, scalable, high-throughput, and well-aligned W/O arrays with excellent long-term stability and predicable droplet sizes have been achieved.