Methods and systems for surface modification are described. In an embodiment, a method of etching includes providing a substrate having a device structure, portions of which are identified for modification. Such a method may also include passivating target surfaces of the device structure by exposing the device structure to a gas-phase composition at a processing pressure equal to or greater than 100 mTorr to form a protection layer on the target surfaces. Other embodiments of a method may include providing a substrate having a device structure, portions of which identified for removal. Such methods may further include passivating target surfaces of the device structure by exposing the device structure to a gas-phase composition, wherein the ratio of the radical content to the ion content exceeds 10-to-1.