Ion beam mixing was applied to produce tungsten carbide nano-layers in C/W nano-multilayer structures, which was studied by Auger electron spectroscopy depth profiling. The destructive AES depth profiling caused serious artefacts such as tungsten-carbide production at the interfaces, even when choosing the optimal sputter removal conditions. Here we show that ion mixing due to the AES depth profiling could be described by TRIDYN simulation, and compound formation could be also estimated by introducing a simple model. Thus, despite the serious artefact production the original pristine depth distribution could be reconstructed. This evaluation method has been checked on C/W layer systems containing tungsten-carbide enrichment in the interface region (due to high energy ion beam mixing); the true in-depth distribution could be reconstructed. It has been found also that with increasing carbide formation the artefact production decreases allowing the use the AES depth profiling without reconstruction.