Recently, the activity on functionalized nano-objects has strongly increased. Yet, there are, to our knowledge no techniques available that visualize the attachment of molecules to nano-entities such as nanoparticles and graphene. In this work, we show a methodology to analyse the attachment of molecules to nanoparticles and graphene. The difficulty of such transmission electron microscopy (TEM) characterization consists in the high beam sensitivity of these nanoobjects. We employed a high resolution- as well as diffraction contrast-imaging methods to characterize graphene. First, we have developed a method to measure the thickness of free-standing graphene-like layers. The refinement of these imaging techniques enabled the imaging of functionalized C60 (fullerene) on top of a few-layer graphene flake by TEM. We also developed a methodology to visualize the attachment of functionalized gold and magnetic nanoparticles (different sizes) to nonstained and unlabeled single strand DNA-coils. This technique can be used to understand the interaction of a large variety of functionalized nanoparticles with their solution environment and/or macromolecular structures for their large applications.