Scanning electron microscope (SEM) has been widely used for characterization and manipulation in micro/nano field. However, existing SEMs can only provide images for samples from one single direction. This limitation sometimes would lead to misleading results. In order to provide multidirectional SEM imaging, a nanorobotic manipulation system with a rotation robot is designed and integrated with SEM. During the robot's rotation, samples fixed on the robot can be viewed by SEM from multi-direction, instead of one direction. The rotation robot is able to rotate 360° along one rotation axis. To facilitate the multidirectional imaging, an automatic alignment method is put forward. This automatic alignment is to align samples to the rotation robot's rotation axis, so that during rotation, samples wouldn't move out of SEM's field of view (FOV). Alignment results are given to justify the proposed alignment method. Magnetic wires have been observed from multi-direction to demonstrate the nanorobotic manipulation system's potential application in micro/nano defect study.