This paper proposes an efficient handing over from the internal stabilization to the external tracking control of a magnetically levitated platform, enabling precise robot-based measurements of free form surfaces. The platform prototype comprises two different sensor systems. The internal sensor system is used to stabilize the platform in a free-floating position with respect to the supporting frame (internal position control), while the external one enables the active compensation of disturbing vibrations by tracking a sample surface (external position control). Based on a cross-fading error gain, the control structure for each out-of-plane DoF comprises a single PID position controller for both control tasks of the platform. Measurement results demonstrate the platform’s capability of performing a simultaneous control transition in the out-of-plane DoFs, while it is stabilized in-plane. Different transition functions are applied to the cross-fading error gain. The findings show that a minimum jerk trajectory performs best regarding transition time and cross-coupling. Using this minimum jerk transition, the translational and rotational positioning errors in the three stabilizing in-plane DoFs are kept below 137 nm rms and 2.05 $\mu$rad rms, respectively.