The atomic structure and atomic scale roughness of GaAs(001)2x4 surfaces fabricated by molecular beam epitaxy was examined by scanning tunneling and atomic force microscopy. In particular, the size and spatial distribution of atomic steps at the surface was quantitatively determined as a function of annealing time and annealing temperature. Two different, parameters are required to fully describe the surface roughness. In general, we found that prolonged annealing under vacuum of surfaces produced by thermal desorption of As cap layers is sufficient to reduce the surface roughness to that typical of as-grown surfaces.