Roll-to-roll nanoimprinting is an emerging technology that has revolutionized the sectors of flexible electronics, thin films, and solar cells with its high throughput. However, there is still room for improvement. In this study, a FEM analysis (in ANSYS) was carried out on a large-area roll-to-roll nanoimprint system in which the master roller consists of a large nanopatterned nickel mold joined to a carbon fiber reinforced polymer (CFRP) base roller using epoxy adhesive. Deflections and pressure uniformity of the nano-mold assembly were analyzed under loadings of different magnitudes in a roll-to-roll nanoimprinting setup. Optimization of deflections was performed with applied loadings, and the lowest deflection value was 97.69 nm. The adhesive bond viability was assessed under a range of applied forces. Finally, potential strategies to reduce deflections were also discussed, which can be helpful in increasing pressure uniformity.