Nanopaper is a new material concept composed of nanocellulose, which has been proposed for a series of applications. Recently, the surface of nanopapers has also been emphasized as an important structure to control. This is due to the potential of nanopaper structures as a substrate for printing functionality, which could expand the applicability of nanopaper as a functionalized biomaterial. In this study, we demonstrate how the roughness of nanopaper is affected by the fraction of residual fibres that were not fibrillated into nanofibrils after a homogenization procedure. The topography and morphology were assessed with laser profilometry, atomic force microscopy and scanning (transmission) electron microscopy. The results show a linear correlation between the estimated fraction of residual fibres and the roughness of the assessed nanopapers. Furthermore, the fraction of residual fibres can be reduced by fractionating the nanocellulose, which is demonstrated in the present work. Such knowledge will be valuable for designing nanopaper surfaces with specific structural characteristics.