Atomic force microscopes (AFMs) are used forsample imaging and characterization at nanometer scale. In thiswork, we consider a metrological AFM, which is used for thecalibration of transfer standards for commercial AFMs. Themetrological AFM uses a three degree-of-freedom (DOF) stageto move the sample with respect to the probe of the AFM. Therepetitive sample topography introduces repetitive disturbancesin the system. To suppress these disturbances, repetitive control(RC) is applied to the imaging axis. A rotated sample orientationwith respect to the actuation axes introduces a non-repetitivenessin the originally fully repetitive errors and yields a deterioratedperformance of RC. Directional repetitive control (DRC) isintroduced to align the axes of the scanning movement with thesample orientation under the microscope. Experiments show thatthe proposed directional repetitive controller significantly reducesthe tracking error as compared to standard repetitive control.