An improved nanomanipulation system is provided for performing nanomanipulation operations in relation to a sample surface. The system includes: an atomic force microscope having a probe for performing nanomanipulation operations on the sample surface, where the probe includes a cantilever having a layer of piezoelectric material; a position detector configured to ascertain deformation of the cantilever during a nanomanipulation operation; and an adaptable end effector controller adapted to receive data indicative of the deformation from the position detector and implements a control scheme based on the deformation data. The control scheme produces a control signal that is applied to the piezoelectric material of the cantilever, thereby maintaining the straight shape of the cantilever during the nanomanipulation operation.