The sizes of silicon nanoparticles produced using two different novel methods are investigated in this report. The method of production used to generate silicon oxide nanoparticles was achieved via gas aggregation codeposition with water on a cold target, and also via a liquid jet method. The nanoparticles were drop-cast on a highly oriented pyrolytic graphite (HOPG) substrate and assessed using ultrahigh vacuum atomic force microscopy (AFM). Noncontact constant force mode was used in the AFM investigations. The silicon nanoparticles produced using the gas aggregation and water codeposition method were found to be smaller than 2 nm. A degree of deviation in the measured sizes of the silicon nanoparticles in different layers was detected. The size deviation was attributed to surface-nanoparticle, surface-tip, and nanoparticle-tip interactions. Silicon nanoparticles produced in alcohol using the liquid jet method were also found to be smaller than 2 nm. The solvent used for the silicon nanoparticles was varied in our investigations. When water was used as a solvent, a size deviation for silicon nanoparticles in different layers was also observed.