The use of tapping mode atomic force microscopy as a sizing tool for nanoparticles is investigated. Height of CdSe nanocrystals measured on different substrates is found to be significantly lower than the particle diameters as determined by transmission electron microscopy. Only minor height variations were found upon particle surface ligand exchange, but significant height variations were found for particles imaged on surfaces with different chemical natures. The distorted height data is attributed to shifts of the tip resonance frequency during imaging, induced by the attractive capillary forces near the substrate. Particle height variations observed when using different drive frequencies of the cantilever corroborate this assignment.