Traditional robotic systems have proven to be instrumental in object manipulation tasks for automated manufacturing processes. Object manipulation in such cases typically involves transport, pick-and-place and assembly of objects using automated conveyors and robotic arms. However, the forces at microscopic scales (e.g., surface tension, Van der Waals, electrostatic) can be qualitatively and quantitatively different from those at macroscopic scales. These forces render the release of objects difficult, and hence, traditional systems cannot be directly transferred to small scales (below a few millimeters). Consequently, novel micro-robotic manipulation systems have to be designed to take into account these scaling effects. Such systems could be beneficial for micro-fabrication processes and for biological studies. Here, we show autonomous position control of passive particles floating at the air-water interface using a collective of self-organized spinning micro-disks with a diameter of 300μm . First, we show that the spinning micro-disks collectives generate azimuthal flows that cause passive particles to orbit around them. We then develop a closed-loop controller to demonstrate autonomous position control of passive particles without physical contact. Finally, we showcase the capability of our system to split from an expanded to several circular collectives while holding the particle at a fixed target. Our system’s contact-free object manipulation capability could be used for transporting delicate biological objects and for guiding self-assembly of passive objects for micro-fabrication.