The ability to accurately determine the size of nanoparticles in the size range of 1-100 nm is essential to the analysis of their size-dependent properties and characteristics. This is typically obtained through Transmission Electron Microscopy (TEM). However, it is difficult for TEM to provide the complete information when the nanoparticles are encapsulated with organic shells. This presentation describes the results of determination of nanoparticle sizes using Tapping Mode Atomic Force Microscopy (AFM). Highly-monodispersed gold nanoparticles of 1-100 nm diameters with well-defined molecular encapsulation were studied as model system. While the lateral size feature was distorted due to the tip convolution effect, the vertical dimension provided quite accurate measurement of the particle size. The correlation between the AFM data and the results obtained by TEM will be discussed, along with its implications to the structures and interactions of the capping molecules.