The silicon trench etching in BCl3/Cl2 reactive ion etching plasma leads to the intrinsic bonding damage, the permeations of etching species and impurities into silicon substrates, and the deposition of residue film on trench sidewall. The contaminations and the damages in trench were investigated by using high resolution transmission electron microscopy (HRTEM), secondary ion mass spectrometry (SIMS), and x-ray photoelectron spectroscopy (XPS). The microstructure of the rounded bottom surface showed that the surface region was distorted by 2 - 6 atomic layers and the trench etch was mainly limited by the physical sputtering-like mechanism. The damage in the silicon lattice consisted of prominent planar defects roughly confined to {110} and {111} planes. The thickness of sidewall residue film was 10 - 90 nm, which was thinner at deeper region of the trench, whereas that of residue film at the trench bottom was 1.5 - 3.5 nm. The SIMS results of no-patterned specimen presented that the permeation depths of boron and chlorine into the Si-substrate were about 40 and 20 nm, respectively. The presence of BxCly and Cl-related Si chemical states was identified from XPS analysis of the residue film.