AAO template is an ideal tool for the fabrication of an array of multiple dots. Here is the schematic drawing of the preparation of the array of multiple dots using ultrathin AAO template.

Fig. 1 (left) Schematic drawing of the preparation of the array of multiple dots using ultrathin AAO template. (up, right) SEM images of an array of multiple dots of Au. (bottom, right) scanning Auger microprobe image of the array of bimetallic dots of Au and Ag. The signals from Au, Ag, and Si are shown in green, red, and blue, respectively.

In Fig. 1, an idealized schematic of the fabrication of an array of multiple dots is shown. After the mask had been placed on the substrate, the metal was evaporated at an appropriate off normal incident angle. The appropriate angle for the spatially resolved deposition, enabled that half of the incident beam was shadowed by the wall of the holes. The second evaporation was performed by changing the incident angle of the metal beam.

Reference: 

Advanced Materials 12,1031-1033 (2000).

http://onlinelibrary.wiley.com/wol1/doi/10.1002/1521-4095(200007)12:14<1031::AID-ADMA1031>3.0.CO;2-R/abstract