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We present the results of calculations performed to simulate the process of atomic-scale imaging and manipulation that explicitly take into account dynamical processes occurring at the surface. These calculations are performed using a novel multi-scale method that combines a simulation of the experimental instrument coupled with a kinetic Monte Carlo simulation of the microscopic system that evolves in real time. This method is applied to three qualitatively different systems: the manipulation of a Pd atom adsorbed on the MgO (001) surface, the imaging of the thermally induced motion of a water molecule adsorbed on the CeO2 (111) surface, and the manipulation of a C60 molecule on the Si (001) surface. The results of these simulations show how optimum protocols for controlled atomic-scale manipulation can be determined and how dynamical surface processes can significantly affect the contrast seen in NC-AFM images.