The subcellular visualisation of nanomaterials is crucial for a wide range of studies in nanomedicine and nanotoxicology. Although light microscopy usually requires less demanding sample preparation, compared to electron microscopy, it suffers from occlusion and resolution when observing nanoparticles. A main difference in the sample preparation is the reduction of cell’s thickness. Here we propose an improved light microscopy setting in which cells are spread on nanostructured patterns as to minimise their thickness, and at the same time minimise the overlap of nanoparticles themselves. Nanostructured substrates were prepared by depositing functionalised gold-RGD nanodots. We optimise the experimental conditions as to minimise cell’s thickness, which literally flattens the cell for further imaging procedures. The improved conditions are attained when cells reach their maximum spreading, and it is found when the dot-dot distance is 58nm. A threshold mechanism in cell adhesion is explained. When cells are maximally flat, confocal microscopy can easily detect the subcellular location of individual carbon nanotubes. This is a novel imaging concept with many potential applications in nanosciences, especially when a fast, reliable and inexpensive visualisation of nanoparticles is required.