The surface modification process with low energy electron beams, generated with a scanning tunneling microscope, is investigated using graphite as an example. By analyzing the cross-sectional profiles, it is shown that local transport properties could play a vital role in determining the characteristics of the fabricated craters. In addition, the observed asymmetry in the contours of the as-produced craters is proposed to be correlated with the geometry of the tip apex region. It is therefore suggested that one look into the roles of low energy electrons, together with the effects of strong electric field, in the fabrication process.