In modern semiconductor device fabrication, the dimensions involved means that Atomic Level Processing, exemplified by Atomic Layer Deposition (ALD), is widely used for film deposition. Further scaling and use of complex three-dimensional structures means that Thermal Atomic Layer Etch (tALE) will start to take centre stage in etching. The key chemistry takes place at surfaces which drives the self-limiting characteristics and other advantages of these atomic level processing approaches. I will present examples to show how first principles atomistic simulations based on Density Functional Theory can be used to predict the chemistry of atomic level deposition and etch processes. I will first discuss the key chemistries involved in atomic level processing chemistries and how these can be accessed by a range of atomistic simulation tools, together with challenges that we have identified in this exciting area. The first scientific topic is the simulation of plasma enhanced deposition (PE-ALD) of metals, using the example of cobalt for next generation interconnects. This is the first example of an atomistic level study of the full PE-ALD cycle for Co metal and show that the process requires use of ammonia or mixed H2/N2 plasma. Calculated energy barriers for key steps give guidance regarding the temperatures required for the process. Finally, we show how substrate pre-treatment can reduce nucleation delay and therefore allow selectivity in deposition of the target film. The second example is MLD of hybrid materials, using alucone and titanicone as the prototypical examples. Using aliphatic ethylene glycol and glycerol results in less-than-ideal growth per cycle (they lie flat) and poor ambient stability. Therefore, we developed functionalized benzene rings as rigid alternatives and show that the molecules remain upright, which provides high GPC and stability. Subsequent work on titanicones with both DFT and experiment, using these aromatic precursors, confirms the enhanced stability of MLD films which also show high growth rates. Finally, I present our work on self-limiting thermal atomic layer etching (ALE), highlighting how simulations can (1) predict the window of self-limiting etch (2) unravel the difference between amorphous and crystalline substrates and (3) probe the impact of surface orientation on tALE chemistry, all of which are important for future thermal ALE processing on complex 3D substrates.