Gratings and step height standards are useful transfer standards for lateral and vertical length scale calibration of atomic force microscopes (AFMs). In order to have traceability to the SI-meter, the standards must have been calibrated prior to use. Metrological AFMs (MAFMs) with online laser interferometric position measurements are versatile instruments for the calibrations. The developed task-specific measurement strategies for step height and pitch calibrations with the Centre for Metrology and Accreditation’s (MIKES’s) metrological AFM are described. The strategies were developed to give high accuracy and to reduce measurement time. Detailed uncertainty estimations for step height and grating pitch calibrations are also given. Standard uncertainties are 0.016 and 0.018 nm for 300 and 700 nm pitch standards, respectively, and 0.21 and 0.44 nm for 7 and 1000 nm step height standards.