This disclosure relates to a plasma processing system and methods for high precision etching of microelectronic substrates. The system may include a plasma chamber that may generate plasma to remove monolayer(s) of the substrate. The plasma process may include a two-step process that uses a first plasma to form a thin adsorption layer on the surface of the microelectronic substrate. The adsorbed layer may be removed when the system transitions to a second plasma or moves the substrate to a different location within the first plasma that has a higher ion energy. In one specific embodiment, the transition between the first and second plasma may be enabled by changing the position of the substrate relative to the source electrode with no or relatively small changes in plasma process conditions.