The aim of this investigation was to characterise the performance of the gas-cluster ion source (GCIS) for the depth profiling of thick organic multi-layer materials. The sample is composed of 25 repeating units of polystyrene (PS) and polyvinylpyrrolidine (PVP) PS = 288 ± 1.3 and PVP = 328 ± 7 nm on a glass substrate. It has been considered challenging to depth profile thick samples (>1 micron) of soft materials due to the changes which occur under sus-tained X-ray irradiation and bombardment of charged projectiles, however, in this study we describe a methodology to eliminate these issues. The use of fast acquisition, snapshot spectroscopy and sample rotation during etching is presented.