This paper proposes a feedforward compensation approach of scan-induced disturbances to improve the uncertainty of an active-sample tracking 3D measurement module. The measurement module acts as a robotic end-effector and is designed for precise robotic measurement applications directly in the vibration-prone environment of an industrial production line. By means of a feedback control-induced stiff link, a constant position of the electromagnetically levitated measurement platform (MP) is maintained with respect to the sample surface under test. Precise 3D imaging is enabled by scanning the measuring light spot of a 1D confocal chromatic sensor with a 2D fast steering mirror (FSM). Disturbances are caused due to scanning-induced reaction forces on the MP, impairing the system’s sample-tracking and 3D measurement performance. Based on the identified disturbance dynamics, a tailored feedforward control is designed to compensate the causing reaction forces. To experimentally evaluate the system performance, 3D measurements at the maximum frame of 1fps are performed with disabled and enabled feedforward control. Evaluating the experimental results, the sample-tracking error in the MP’s translational degree of freedom z is significantly reduced by a factor of 7 down to 42nm rms, being close to the MP’s static positioning noise. The reduced sample-tracking error further enables a higher 3D measurement performance, reducing the structural height uncertainty by 36% down to 180nm rms.