Methods and apparatus are disclosed for concurrent cleaning and cleanliness monitoring of a sample such as a substrate for electron point projection microscopy. A graphene sample is illuminated by a laser. Raman scattering from contaminants generates secondary light which is analyzed by spectrometer. Based on Raman scattering analysis, sample cleanliness is determined. Cleaning can be dynamically terminated based on achieving a target cleanliness level or based on prediction thereof. Variations and additional applications are disclosed.