X-ray photoelectron spectroscopy (XPS) was used in conjunction with gas cluster ion source etching to analyze polystyrene and polyvinylpyrrolidone multilayer samples, total thickness~15 μm, to establish optimal conditions for depth profiles over many μm in depth. Using standard conditions, these samples demonstrate a reduction in depth resolution and sputtering yield, which is shown to be partly due to X-ray-induced damage and partly due to roughening of the sputtered surface. By limiting the X-ray exposure, it was possible to retain depth resolution to a depth of approximately 5 μm; to obtain useful depth profiles beyond this depth, it was necessary to use sample rotation. The use of optimized conditions allowed the chemical integrity of the polymer layers to remain intact during the etching process with relatively sharp interfaces over the full depth of the films. Both the elemental intensities in XPS and the line shape of the C 1s peak could be used to determine the differences in chemical structure of the films in the depth profile.Detailed analysis suggests that a "stepwise" rotation scheme can maintain depth resolution better than continuous rotation during sputtering.