A damage-reduced trench was investigated in view of the defect distribution along trench sidewall and bottom using high resolution transmission electron microscopy, which was formed by HBr plasma and additive gases in magnetically enhanced reactive ion etching system. Adding $O_2$ and other additive gases into HBr plasma makes it possible to eliminate sidewall undercut and lower surface roughness by forming the passivation layer of lateral etching. To reduce the RIE induced damage and obtain the fine shape trench corner rounding, we investigated the hydrogen annealing effect after trench formation. Silicon atomic migration on trench surfaces using high temperature hydrogen annealing was observed with atomic scale view. Migrated atoms on crystal surfaces formed specific crystal planes such as (111), (113) low index planes, instead of fully rounded comers to reduce the overall surface energy. We could observe the buildup of migrated atoms against the oxide mask, which originated from the surface migration of silicon atoms. Using this hydrogen annealing, more uniform thermal oxide could be grown on trench surfaces, suitable for the improvement of oxide breakdown.