The issue of functional surfaces consisting of multi-scale structures is under active discussion. Common examples of these are superhydrophobic surface, antireflective film, cell-culturing plate and so on. At the same time, the research on manufacturing methods to mass production of functional surfaces is also in progress. In the present study, injection compression molding (ICM) process was applied in order to manufacture the multi-scale structures. Under ICM, the transcription ratio of micro-structure at the farthest point from the gate was almost 35% higher than that obtained by conventional injection molding (CIM) for a specific experimental condition. We investigated micro-scale filling behavior in ICM through multi-scale simulation. The simulation procedure consists of two steps; as the first step, pressure history data were exported from the macro-scale flow simulation in which the numerical domain was considered as 7 inch geometry with a thickness of 0.5 mm. As the second step, the micro-scale flow simulation was performed using macro-scale pressure data as the boundary conditions. The micro-scale domain contains single cylindrical micro-feature with a diameter of 30 μm and a depth of 14 μm on the nickel stamper. In conclusion, the numerical results show that enhancement of the transcription ratio of micro-structure by ICM is attributed to the difference in the packing mechanism between CIM and ICM.