The ability to generate a large area micropillar array with spatially varying heights allows for exploring numerous new interesting applications in biotechnology, surface engineering, microfluidics, and so forth. This Letter presents a clever and straightforward method, called electrically modulated microtransfer molding (EM3), for generating such unique microstructures from a silicon mold arrayed with microholes. The key to the process is an application of electrically tunable wettability caused by a spatially modulated voltage, which electrohydrodynamically drives a photocurable and dielectric prepolymer to fill the microholes to a depth depending on the voltage amplitude. Using EM3, micropillar arrays with stepwise or continuously varying heights are successfully fabricated, with the diameter scalable to 1.5 μm and with the maximum height being equal to the depth of the high-aspect-ratio (more than 10:1) microholes.