The pervasive phenomenon of friction has been studied at the nanoscale via a controlled manipulation of single atoms and molecules with a metallic tip, which enabled a precise determination of the static friction force necessary to initiate motion. However, little is known about the atomic dynamics during manipulation. Here, we reveal the complete manipulation process of a CO molecule on a Cu(110) surface at low temperatures using a combination of noncontact atomic force microscopy and density functional theory simulations. We found that an intermediate state, inaccessible for the far-tip position, is enabled in the reaction pathway for the close-tip position, which is crucial to understanding the manipulation process, including dynamic friction. Our results show how friction forces can be controlled and optimized, facilitating new fundamental insights for tribology.