With a vertical resolution of 0.1 nm, atomic force microscopy (AFM) height measurements can be used to determine accurately the diameter of single-walled carbon nanotubes (SWNT) with the assumption that they have circular cross sections. The aim of this article is to draw attention to the need to optimize operating parameters in tapping mode for quantitative AFM height (diameter) analysis of SWNTs. Using silicon tip/cantilever assemblies with force constants ranging from 0.9 to 40 N m−1, we examined the effect of applied force on the apparent diameter of SWNT wrapped with a 29-residue amphiphilic α-helical peptide. A decrease in apparent height (SWNT diameter) with increasing applied force was observed for the higher force constant cantilevers. Cantilevers having force constants of 0.9 and 3 N m−1 demonstrated minimal vertical sample compression with increasing applied force. The effects of AFM image pixel density and scan speed on the measured height (diameter) of SWNTs were also assessed.