The paper aims to present a mechatronic device able to micro-position the workpiece and to reject disturbances due to machining operation. A decoupling method is proposed for a parallel kinematic machine (PKM) fixturing platform composed by a 3-DoF flexure-based piezo-actuated mechanism. The parallel platform, with a vertical motion and two rotations, is described and its kinematics and dynamics are studied. The coupling undesirable effect is investigated based on a set of poses. To improve the quasi-static regulator model for a set-point following system, a bump less switching controller and a fine-tuning procedure, to estimate the parameter uncertainty and enable the external disturbance containment in an extended broadband frequency range, are presented. The platform and the piezo-actuator controllers are modelled based on a gain scheduling, standard ISA form method, to guarantee the stability. The accuracy is demonstrated through a set of simulations and experimental comparisons. A sensitivity analysis that evaluates the tracking performance and the disturbance rejection based on the number of signal amplitudes, frequencies, and phases is discussed. A validation phase has shown that the developed architecture presents a steady state error lower than 1.2 µm, a vibration reduction of 96% at 1130 Hz with a maximum resolving time of 6.60 ms.