There is currently a lack of understanding of the deposition profile in a batch atomic layer deposition (ALD) process. Also, no on-line control scheme has been proposed to resolve the prevalent disturbances. Motivated by this, we develop a computational fluid dynamics (CFD) model and an integrated online run-to-run and feedback control scheme. Specifically, we analyze a furnace reactor for a SiO2 thin-film ALD with BTBAS and ozone as precursors. Initially, a high-fidelity 2D axisymmetric multiscale CFD model is developed using ANSYS Fluent for the gas-phase characterization and the surface thin-film deposition, based on a kinetic Monte-Carlo (kMC) model database. To deal with the disturbance during reactor operation, a proportional integral (PI) control scheme is adopted, which manipulates the inlet precursor concentration to drive the precursor partial pressure to the set-point, ensuring the complete substrate coverage. Additionally, the CFD model is utilized to investigate a wide range of operating conditions, and a regression model is developed to describe the relationship between the half-cycle time and the feed flow rate. A run-to-run (R2R) control scheme using an exponentially weighted moving average (EWMA) strategy is developed to regulate the half-cycle time for the furnace ALD process between batches.