The evolution of surface cleanliness and the electronic properties-Dirac voltage(VDirac), hysteresis and mobility (μ) of a graphene field-effect transistor (GFET)—were monitored by measuring lateral force microscopy and drain current (ID) as a function of gate voltage (VG), after mechanically cleaning the surface, scan-by-scan, with contact-mode atomic force microscopy. Both the surface cleanliness and the electronic properties evolved, showing a sudden improvement and then saturation for a mobility of around 2200 cm2 V−1 s−1. We found that the mobility suppression of the as-fabricated GFET deviated from a randomly distributed impurities model, which predicted a greater mobility than obtained from the measured VDirac. Therefore, the substrate impurities are excluded from the origins of the extraordinary suppression of the mobility, and the possible origin will be discussed.