Controller design to compensate vibration, hysteresis and time delay in a high-speed serial-kinematic X-Y nanopositioner is presented in this paper. A high-speed serial-kinematic X-Y nanopositioner, designed in-house, is installed in a commercial AFM and its scanning performance is studied. The impediments to fast scanning are (i) the presence of mechanical resonances in the nanopositioning stage, (ii) nonlinearities due to the piezoelectric actuators and (iii) time delay introduced by finite clock speeds of the signal conditioning circuitry associated with displacement sensors. In this paper an integral resonant controller is designed to mitigate the effect of the resonance along the X axis (fast axis). The control design accommodates for the time delay, thereby ensuring robust stability. A high gain integral controller is wrapped around the damped nanopositioner to ensure sufficient linearity near the region of operation. For actuation along the Y axis (slow axis), where the bandwidth requirement is less demanding, a notch filter is used to increase the gain margin and the nonlinearity is compensated using a high gain feedback controller. Enhancement in the scanning speed up to 200 Hz is observed. Imaging and tracking performance for open loop and closed loop scans up to 200 Hz line rate is compared and presented. Limitations and future work are discussed. © 2014 IOP Publishing Ltd.