Fluorophores or other indicators can be used to label and identify one or more defects in a graphene layer by localizing at the one or more defects and not at other areas of the graphene layer. A substrate having a surface at least partially covered by the graphene layer may be contacted with the fluorophore such that the fluorophore selectively binds with one or more areas of the surface of the underlying substrate exposed by the one or more defects. The one or more defects can be identified by exposing the substrate to radiation. A detected fluorescence response of the fluorophore to the radiation identifies the one or more defects.