Roll-to-roll (R2R) printing process is a key technology for achieving low-cost mass production of multilayer printed electronic devices. A register control, which maintains position accuracy between layers, is essential in the R2R multilayer printing process. In this study, a register control algorithm is developed to achieve microscale resolution in the register. The dominant factor behind machine direction register error is determined. Furthermore, an adequate register model is determined to estimate the register error according to tension disturbances. Permissible tension error is achieved for accomplishing the objective register and minimized for register control. The effect of the developed algorithm on the resolution of the register control is verified experimentally. Experimental results indicate that applying the proposed register algorithm achieved resolution below ±30µm. This suggests that the proposed register algorithm is an essential application for a microscale resolution register. Finally, an application of the algorithm was introduced using examples considered in previous researches.