The superconducting flux flow transistor (SFFT) with three-channel was successfully fabricated by an electron beam lithography and Ar ion milling technique. In our paper the cross sectional analysis and topological views are investigated for the channel width and the channel height by the atomic force microscopy (AFM) image. Our result shows that the SFFT of multi-structure with a nano-channel is effectively fabricated by an electron-beam lithography method. We present a fabrication process of three-channel SFFT using the electron beam lithography. Mechanisms of nano-channel SFFT are studied.