Web deformation occurring in the ink transfer process from the printing roller to the flexible web was investigated using a CFD technique for the application in roll-to-roll printed electronics. Analysis for the flow-structure interaction was conducted to assess the deflection and stress distributions of the web. To make the present analysis more relevant to the real printing system, both realistic geometric configuration and ink properties were set up using the information obtained from the typical roll-to-roll system. Fluid properties were found to influence to the shape of the transferred ink and the web deformation. As the line width becomes smaller than 100 microns, the appreciable distortion in the shape of the transferred ink occurred due to a relative importance of surface tension. Non-negligible web deflection occurs in all the cavity geometries considered in the present work but the ratio of the web deflection to the line width gets smaller as the printing pattern width becomes smaller. Thus, the surface and deflection will be important factors for the better printing quality under the 100 micron range.