The combination of self-assembly (bottom up) and nano-imprint lithography (top down) is an efficient and effective way to record information at the nanoscale by writing. The use of an electron beam for writing is quite a promising strategy; however, the ‘paper’ on which to save the information is not yet fully realized. Herein, graphene was selected as the thinnest paper for recording information at the nanoscale. In a transmission electron microscope, in situ high precision writing and drawing were achieved on graphene nanosheets by manipulating electrons with a 1 nm probe (probe current ∼2 × 10−9 A m−2) in scanning transmission electron microscopy (STEM) mode. Under electron probe irradiation, the carbon atom tends to displace within a crystalline specimen, and dangling bonds are formed from the original sp2 bonding after local carbon atoms have been kicked off. The absorbed random foreign amorphous carbon assembles along the line of the scanning direction induced by secondary electrons and is immobilized near the edge. With the ultralow secondary electron yield of the graphene, additional foreign atoms determining the accuracy of the pattern have been greatly reduced near the targeting region. Therefore, the electron probe in STEM mode serves as invisible ink for nanoscale writing and drawing. These results not only shed new light on the application of graphene by the interaction of different forms of carbon, but also illuminate the interaction of different carbon forms through electron beams.