you mean step-height measurements by AFM? Crystal size has no relation with step height.....even amorphous carbon films can be nano meter thick.. best way to measure crystallite size is from Id/Ig ratio from raman spectra
Actually, measuring thickness of graphene sheets by AFM has many pitfalls(read this paper doi:10.1016/j.carbon.2008.06.022).. though people religiously use this technique to measure thickness of graphene sheets, and its widely accepted !!!..