I guess you are referring to, how you can make it rectangular rather than quadratic. Well, you can't, the tool in it's current design will only generate regular structures. One alternative is to build a 1x1 nm^2 shape and "glue" them together, 2x3. If you use a metallic material or Si or Ge, you could use the EMT or Brenner potentials in ATK-Classical to optimize the so-obtained geometries. Or build a 3x3 nm^2 structure and remove 1 nm in one dimension.