We have studied the effects of the microscopic roughness of a GaAs epitaxial surface on the oxide layer, which is used as a resist-mask material in in situ electron-beam lithography. When electron beam patterning, followed by Cl-2 gas etching, was carried out for an oxide-mask layer formed on a rough surface, an indented pattern edge elongated along the [1(1) over bar0$] direction, typically having a size of several tens of nm, was formed. On the other hand, when we used a misoriented substrate in order to obtain a smooth epitaxial surface by introducing the so-called step-flow growth mode, the resulting pattern exhibited a sufficiently sharp edge. Based on this improvement, together with the optimized electron-beam patterning system, we successfully fabricated an ultrafine trench structure with a width as small as 20 nm.