Size measurements of standard nanoparticles using metrological atomic force microscope and evaluation of their uncertainties

•Size of standard nanoparticles was measured using the metrological atomic force microscope.•The uncertainty in particle size measurement was evaluated.•Particle deformations were calculated based on the assumption of plastic deformation between particles and a substrate.•The uncertainties derived from the particle deformation were also evaluated.•The metrological AFM measurement results were compared with those of other microscopy methods.