A self-assembled monolayer (SAM) molecule is attractive as an active region of an electron device because of its inherent small thickness (~1-2 nm) between each electrode. We reported processes to fabricate small Au/SAM/Au junctions by using electron beam lithography. As a SAM molecule, we used benzene-1,4-dithiol on Au. To obtain an atomically flat Au electrode without deformation of shape, lower deposition rate, lower sample temperature, and adequate annealing temperature were required. By using a SiO2 pattern as a shadow mask, twice oblique evaporations made small Au/SAM/Au junctions. A minimum feature size of slit of a SiO2 pattern was 160 nm by using electron beam lithography. Si substrate isolated by SiO2 works as a gate electrode of three terminal devices by the Au/SAM/Au junctions. Observed current-voltage characteristics between the drain and the source showed nonlinear characteristics and weak modulation by gate bias was observed. The processes to improve device characteristics are also discussed.