Polymers are often modified by plasma treatment to adapt them to new applications. During the deposition of an amorphous hydrogenated (a-C:H) layer, a mixed phase (interlayer) of the polymer substrate and the deposited layer often forms. The interlayer is responsible among others for a good adhesion between the layer and the substrate. In this study, amorphous hydrogenated carbon films were deposited on the structurally similar biopolymers polylactic acid (PLA) and polyhydroxybutyrate (PHB) using radio frequency plasma enhanced chemical vapor deposition (RF-PECVD). In an industrially established process, layer thicknesses of up to 50 nm were produced in 10 nm steps. The surface morphology of each layer was investigated by ex situ atomic force microscopy. Chemical composition was explored first with surface sensitive synchrotron X-ray-based techniques such as X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure. Subsequently, IR measurements were performed for a more detailed analysis of the functional groups contained. Based on the data obtained (e.g. sp2/sp3 ratio, grain formation on the surface), it was possible to determine the transition of polymer to a-C:H layer and therefore the thickness of the interlayer dimension formed during coating. For PLA, the thickness is about 40 nm, for PHB 20 nm.