A three-dimensional hydrogel scaffold has been proposed for the effective production of biomimetic intestinal villi to reduce ethical and cost problems caused by animal testing in pharmaceutical development. This study explores an experimental approach to develop a new technique based on laser machining and microdrilling processes to produce a plastic mold for the fabrication of a three-dimensional hydrogel scaffold. For process optimization, both the laser machining and the microdrilling experiments are conducted by varying the experimental conditions, and structural characterization of the mold and intestinal villi were performed using SEM (scanning electron microscope) and OM (optical microscope) images. Polycarbonate (PC) was used as a candidate material. The experimental results show that intestinal villi can be fabricated by both laser and microdrilling machining processes.