Highly scaled gravure printing has attracted great attention recently because of its high resolution, large throughput, and low cost. Cell filling is the first step in the actual gravure printing process, and it strongly determines the quality of printed patterns. Therefore, systematically studying the impact of cell geometry on the filling process is necessary to better understand and improve gravure printing. In this work, we demonstrate the fabrication details to make cells with different cross-section geometries, a novel setup that provides filling details for sub-5 μm cells in real-time to understand the geometry impacts on cell filling process, and a model that helps to predict the filling failure regimes. Cell filling fails when the ink cannot replace air inside the cells completely, because this may result in discontinuous lines and non-uniform films in printed patterns. By varying the viscosity and flow speed of the fluid, we conclude that the dimensionless capillary number is a good indicator for this cell filling study. Cell filling fails for round shape and pyramid shape cells at high capillary numbers, and a unique “advancing filling” phenomenon occurs for round shape cells at low capillary numbers. The round shape cells can be filled at higher capillary numbers than pyramid shape cells, so this type of cell geometry can potentially be applied in future gravure printing master designs. Square shape cells are difficult to be filled, even at small capillary numbers, and therefore should not be used in gravure printing.