We developed a novel nano manipulator based on an atomic force microscope (AFM) that can be operated inside the sample chamber of a scanning electron microscope (SEM). This AFM manipulator is also coupled with a haptic device, and the nanometer-scale movement of the AFM cantilever can be scaled up to the millimeter-scale movement of the pen handle of the haptic device. Using this AFM manipulation system, we were able to observe the AFM cantilever and samples under the SEM and obtain topographical images of the AFM under the SEM. These AFM images contained quantitative height information of the sample that is difficult to obtain from SEM images. Our system was also useful for positioning the cantilever for accurate AFM manipulation because the manipulation scene could be directly observed in real time by SEM. Coupling of the AFM manipulator with the haptic device was also useful for manipulation in the SEM since the operator can move the AFM probe freely at any position on the sample surface while feeling the interaction force between the probe and the sample surface. We tested two types of cutting methods: simple cutting and vibration cutting. Our results showed that vibration cutting with probe oscillation is very useful for the dissection of biological samples which were dried for SEM observation. Thus, cultivated HeLa cells were successfully micro-dissected by vibration cutting, and the dissection process could be observed in real time in the SEM. This AFM manipulation system is expected to serve as a powerful tool for dissecting various biological samples at the micro and nanometer-scale under SEM observation.