Silver nanoparticles were sputter deposited through self organized hexagonally ordered porous anodic alumina templates that were fabricated using a two-step anodization process. The average pore diameter of the template was 90 nm and the interpore spacing was 120 nm. Atomic force microscope studies of the sputter-deposited silver nanoparticle array on a Si substrate indicate an approximate replication of the porous anodic alumina mask. The nature of the deposition depends strongly on the process parameters such as sputtering voltage, ambient pressure and substrate temperature. We report a detailed study of the sputtering conditions that lead to an optimal deposition through the template.