The complementary capabilities of various characterisation methods for micro-structural assessment are demonstrated. The assessed structures were composed of unbleached microfibrillated cellulose (MFC) in combination with bleached and 2,2,6,6-tetramethylpiperidinyl-1-oxyl (TEMPO) pre-treated MFC materials. The biodegradable nano-composites were thus characterised in detail, including laser profilometry, scanning electron microscopy (SEM) in high and low vacuum modes, and field-emission SEM. The distribution of the unbleached MFC materials was assessed by staining the unbleached MFC with osmium tetroxide (OsO4), which reacts with CC double bonds encountered in lignin. In addition, some properties of the MFC nano-composite films were tested, i.e. tensile properties, water wettability and oxygen permeability. In general, the group of characteristics of the nano-composite MFC films was better than the properties of the films made of the neat MFC qualities. This indicates that mixing complementary MFC qualities could give synergetic effects that are not exploited completely when using the MFC qualities separately. The study thus confirms the suitability of unbleached MFC materials as a component in multilayer structures, for example biodegradable packaging applications.