We report atomic scale flattening of surfaces of microstructures formed on Si wafers by furnace annealing. To avoid thermal deformation of the fabricated structures, advantage was taken of hydrogen annealing, which enables us to decrease the relaxation rate of Si surfaces due to surface hydrogenation. We examined cross-sectional shape and sidewall morphology of 3 mu m deep trenches on Si(001) substrates after annealing at 1000 degrees C under various H-2 pressures of 40-760 Torr. We successfully formed Si trenches with flat surfaces composed of terraces and steps while preserving the designed trench profile by increasing H-2 pressure to 760 Torr. (c) 2005 Elsevier B.V. All rights reserved.