This letter presents a method to determine and control the center of rotation of a parallel micro-robotic platform used as a sample holder for an Atomic Force Microscope (AFM). The AFM is operating inside a Scanning Electron Microscope (SEM) for correlative AFM in SEM imaging. The objective is to spatially co-localize the Pivot Point (PP) and the AFM tip at any region of interest of a sample within the reachable workspace of the AFM. To do so, SEM images are used to land the AFM tip on a desired Point Of Interest (POI). Topographic data obtained with the AFM are used to calculate the Tool Center Point (TCP) of the robot and to identify the coordinates of the POI in the AFM sample holder reference frame. The position of the PP is then controlled relying on the TCP and SEM vision to finally been able to perform, in a controlled way, in-plane rotations of the sample holder around the AFM tip with a micrometer precision. This work shows for the first time how SEM and AFM data can be used in tandem to calibrate the rotational degrees of freedom of an AFM system.