In anisotropic etching of the substrates, ultra-thin and conformable layers of materials can be used to passivate sidewalls of the etched features. Such a sidewall passivation layer may be a Self-assembled monolayer (SAM) material deposited in-situ etching process from a vapor phase. Alternatively, the sidewall passivation layer may be an inorganic-based material deposited using Atomic Layer Deposition (ALD) method. SAM or ALD s layer deposition can be carried out in a pulsing regime alternating with sputtering and/or etching processes using process gasses with or without plasma. Alternatively, SAM deposition is carried out continuously, while etch or sputtering turns on in a pulsing regime. Alternatively, SAM deposition and etch or sputtering may be carried out continuously. Both types of suggested passivation materials give advantage over state-of-the-art methods in ability to carefully control thickness and uniformity of the layers, thus enable anisotropic etching process for high aspect ratio nanosize features.