For a large multi-wafer vertical batch ALD reactor, transient, 3-dimensional, multi-scale simulations have been performed for the TEMAH pulse step during a HfO2 ALD process. A bi-directional, multi-scale coupling has been established between continuum reactor scale simulations and molecular trench scale simulations. For describing the molecular deposition process inside narrow deep trenches, two different models have been developed and implemented as boundary condition for the flow simulation: an analytical model based on the model proposed by Gordon, and a numerical Knudsen diffusion model. Both trench models have been validated against DSMC simulation results for a single trench. Based on the 3D reactor simulation results, important timescales in the complete process are identified. It is found that several timescales are of the same order of magnitude, rendering predictions based on engineering rules more difficult. Timescales for trenched wafers are found to be much larger than for flat wafers, leading to much longer required cycle times.