The suppression of interferences from atomic and molecular isobars is a key requirement for the extension of accelerator mass spectrometry (AMS) to the analysis of new cosmogenic isotopes and for increasing the range of applications for small AMS systems. In earlier work, it was shown that unwanted isobars can be eliminated by anion-gas reactions (Litherland et al. 2007). Recently, a prototype system in which such reactions could be applied to ions from an AMS ion source, the Isobar Separator for Anions (ISA), was described (Eliades et al. 2009). This system decelerates the beam of rare anions from keV to eV energies, guides them through a single radiofrequency quadrupole (RFQ) gas cell, and re-accelerates them for further analysis in a 2.5MV AMS system. Tests of this system with Cl and S anions and NO2 gas showed a suppression of S with respect to Cl of over 6 orders of magnitude, with a transmission of ∼30% for the Cl beam. In this work, results of the analysis of a range of standard reference materials are reported; these show the linearity of the system for measuring the 36Cl/35Cl ratio over a span of 2 orders of magnitude. Further tests, using the AMS system as a diagnostic tool, have provided clues about the loss of Cl at higher cell pressure and the nature of the residual low level of S transmission. These lead to the assessment of various gases for cooling the Cl– beam. Suppression measurements for 41K in the analysis of 41Ca, using NO2 as a reaction gas, are also discussed. These preliminary measurements have provided data for the development of a more advanced system with separate cooling and reaction cells.