Abstract: Due to the small space and invisibility in MSE3, the alignment of MSE3 of separated sector cyclotron remains a longstanding challenging for the aligned personnel. Coupled with the compressed time, to quickly and accurately find MSE3's fault and realign its position is essential for the regular operation of the accelerator. This paper analyzes the principle of MSE3 and its transmission mechanisms, and establishes an effective model to standardize the drive motor. Furthermore, it develops a rapid realignment method based on multiple coordinate system transformation. The method can provide a basis for overhaul and alignment of similar component in related accelerators.