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Ar cluster sputtering of organic multilayers such as organic light‐emitting diode model structures and Irganox delta layers is studied with time‐of‐flight secondary ion mass spectroscopy in the dual beam mode. Results for sputtering yield volumes and depth resolution are presented for Ar clusters with sizes from 500 to 5000 atoms in the energy range from 2.5 to 20 keV. The sputtering yield volume shows a linear dependence on the energy per atom for all materials in this study with a material‐dependent threshold below 1 eV/atom. The sputtering yield volume at a given energy per atom increases with the cluster size. At constant beam energies, the sputtering yield volume decreases slightly with increasing cluster size. The depth resolution is investigated for the two model systems as a function of energy and cluster size, and it will be shown that the depth resolution depends mainly on the sample roughening. The depth resolution is approximately proportional to the depth of the impact crater at a given cluster size and energy. The optimum depth resolution achieved is in the range of 4–5 nm and is fairly constant with depth. At very low energies per atom close to the threshold energy, ripple formation is observed that leads to a fast degradation of the depth resolution with depth. This can be completely eliminated by fast sample rotation. Finally, the perspective of 3D analysis of organic devices with high depth resolution in the dual beam mode will be discussed. Copyright © 2012 John Wiley & Sons, Ltd.