Nanosphere lithography (NSL) is an inexpensive, inherently parallel, high-throughput, and materials-general nanofabrication technique capable of producing well-ordered 2D periodic particle arrays of nanoparticles. This paper focuses on the synthesis of size-tunable silver nanoparticle arrays by nanosphere lithography and their structural characterization by atomic force microscopy (AFM). The in-plane diameter, a, of Ag nanoparticles was tuned from 21 to 126 nm by systematic variation of the nanosphere diameter, D. Similarly, the out-of-plane height, b, was tuned from 4 to 47 nm by varying the mass thickness, d(m), of the Ag overlayer. Experimental measurements of a, b, and interparticle spacing di, of many individual nanoparticles as a function of D and d(m) were carried out using AFM. These studies show (i) b = d(m), (ii) d(ip) accurately corresponds to predictions based on the nanosphere mask geometry, (iii) a, after correction for AFM tip convolution, is governed only by the mask geometry and the standard deviation, sigma(D), of the nanosphere diameter, and (iv) line-of-sight deposition is strictly operative. Furthermore, we have established that nanosphere lithography can fabricate nanoparticles that contain only ca. 4 x 10(4) atoms and are in the size range of a surface-confined cluster.