The gas cluster ion beam (GCIB) and liquid metal ion beam have been studied in the context of ion beam usage for analytical equipment in applications such as X-ray photoelectron spectroscopy and secondary ion mass spectroscopy (SIMS). In particular, small ion sources are used for the secondary ion generation and ion etching. To set the context to this study, the SIMS project has been launched to develop ion-gun based analytical equipment for the Korea Basic Science Institute. The objective of the first stage of the project is the generation of argon beams with a GCIB system [A. Kirkpatrick, Nucl. Instrum. Methods Phys. Res., Sect. B 206, 830-837 (2003)] that consists of a nozzle, skimmer, ionizer, acceleration tube, separation system, transport system, and target. The Wien filter directs the selected cluster beam to the target system by exploiting the velocity difference of the generated particles from GCIB. In this paper, we present the theoretical modeling and three-dimensional electromagnetic analysis of the Wien filter, which can separate Ar(+) 2500 clusters from Ar(+) 2400 to Ar(+) 2600 clusters with a 1-mm collimator.