Replica molding is one of the most common and low-cost methods for constructing microstructures for various applications, including dry adhesives, optics, tissue engineering, and strain sensors. However, replica molding provides only a single-height microstructure from a mold and master molds produced by an expensive photolithography process are required to prepare microstructures with different heights. Herein, we present a strategy to control the height of micropillars from the same mold by varying the cavity size of the micromold and the viscosity of the photocurable polyimide resin. The height of the constructed micropillar decreases in the case of small microcavities or high viscosity resin. In addition, the height of the micropillar arrays could be arbitrarily patterned by applying a masking technique. We believe that this cost-effective technique can be applied to metasurfaces for manipulation of electromagnetic signal or in biomedical applications including cell-culture and stem-cell differentiation.