Graphitic nanodisks of typically 20–50 nm in thickness, produced by the so-called Kvaerner Carbon Black and Hydrogen Process were dispersed on gold substrate and investigated by atomic force microscopy (AFM), field emission scanning electron microscopy (FE-SEM), and confocal Raman spectroscopy. The roughness of the gold surface was drastically changed by annealing at 400 °C. AFM measurements show that this change in the surface roughness induces changes also in the topography of the nanodisks, as they closely follow the corrugation of the gold substrate. This leads to strained nanodisks, which is confirmed also by confocal Raman microscopy. We found that the FE-SEM contrast obtained from the disks depends on the working distance used during the image acquisition by In-lens detection, a phenomenon which we explain by the decrease in the amount of electrons reaching the detector due to diffraction. This process may affect the image contrast in the case of other layered materials, like hexagonal boron nitride, and other planar hybrid nanostructures, too.