Printing in flexible packaging is often done on very thin films whose thickness ranges from 12 micron to more than 100 microns. When the thickness of the printed ink layer approaches the thickness of the film, it often introduces severe roll distortion in normal roll-to-roll applications. This distortion is also observed in a less pronounced manner in applications that use stacking, such as labels and books. This distortion is conventionally managed by reducing the ink-pile height. In digital printing (inkjet and also in xerographic) the pile height problem limits the applicability of printing for flexible packaging applications.In this paper we describe an imaging based for managing pile height that normalizes the surface height across the substrate. The solution proposed here tries to intelligently balance the ink-layer discrepancies across the roll width using image-based compensation so that cylindrical shape of roll is maintained. This enables the film/substrate to advance at a uniform rate, and the differential rolling stress across the substrate cross section to approach the normal operational range. This innovation will enable digital printing to play a more significant role in roll-toroll based packaging applications such as flexible packaging.