The ability to achieve atomic layer precision is the utmost goal in the implementation of atomic layer etch technology. Carbon-based materials such as carbon nanotubes (CNTs) and graphene are single atomic layers of carbon with unique properties and, as such, represent the ultimate candidates to study the ability to process with atomic layer precision and assess impact of plasma damage to atomic layer materials. In this work, the authors use these materials to evaluate the atomic layer processing capabilities of electron beam generated plasmas. First, the authors evaluate damage to semiconducting CNTs when exposed to beam-generated plasmas and compare these results against the results using typical plasma used in semiconductor processing. The authors find that the beam generated plasma resulted in significantly lower current degradation in comparison to typical plasmas. Next, the authors evaluated the use of electron beam generated plasmas to process graphene-based devices by functionalizing graphene with fluorine, nitrogen, or oxygen to facilitate atomic layer deposition (ALD). The authors found that all adsorbed species resulted in successful ALD with varying impact on the transconductance of the graphene. Furthermore, the authors compare the ability of both beam generated plasma as well as a conventional low ion energy inductively coupled plasma (ICP) to remove silicon nitride (SiN) deposited on top of the graphene films. Our results indicate that, while both systems can remove SiN, an increase in the D/G ratio from 0.08 for unprocessed graphene to 0.22 to 0.26 for the beam generated plasma, while the ICP yielded values from 0.52 to 1.78. Generally, while some plasma-induced damage was seen for both plasma sources, a much wider process window as well as far less damage to CNTs and graphene was observed when using electron beam generated plasmas.