The aim of this research is to fabricate Ag nanoparticle assemblies forming nanolayers with different thicknesses in order to evaluate their physical properties and their 3-D (three-dimensional) surface micromorphology. Such Ag nanolayers were deposited by physical vapor deposition methods under ion-beam irradiation in argon atmosphere at room temperature. X-ray diffraction (XRD) characterizations confirmed the formation of silver nanocrystals. Using surface field parameters, which were derived from atomic force microscopy (AFM) analysis, the surface morphology of the nanolayers were described according ISO 25178-2:2012. The height and slope distribution functions, together with the autocorrelation (ACF), the height–height correlation (HHCF) and the power spectral density (PSDF) functions were determined for the different analyzed samples using linear interpolation in the horizontal direction. All samples had a fractal character with a fractal dimension of 2.54 ± 0.01 independent of the film thickness.