For the accurate characterisation of organic layered structures, we suggest a novel methodology to fabricate the bevel structure by utilising specific adjustment condition of the argon cluster ion beam sputtering (Ar GCIB), namely, little chemical damage to the organic material and a spatial gradient of ion dose in the sub-millimeter range. The Ar GCIB sputtering settings are elaborately tuned on the basis of the Faraday/target current, and its optimization condition for preparing the bevel structure is consequently determined. As a standard sample, an organic bevel structure was manufactured from the organic layered structure of C60/SubPC/PEDOT:PSS films, and their molecular distribution and chemical/electronic structures were investigated using various analytical techniques, including X-ray photoelectron spectroscopy, secondary ion mass spectrometry, Auger electron spectroscopy, Raman spectroscopy, and matrix-free ultraviolet-laser desorption/ionization. All the experimental results demonstrate clearly that the bevel structure prepared by our method keeps its original molecular distribution and chemical structure. On the contrary, conventional etching techniques such as Ar+ ion beam, focused ion beam, and ion milling cause critical distortion in chemical information without exception. Ultimately, our suggested method, a unique way to prepare a damage-free organic bevel structure, significantly widens the availability of analytical techniques that have limitations in spatial or depth resolution.