Embodiments described herein relate to apparatus and methods for processing a substrate. In one embodiment, a cluster tool apparatus is provided having a transfer chamber and a pre-clean chamber, a self-assembled monolayer (SAM) deposition chamber, an atomic layer deposition (ALD) chamber, and a post-processing chamber disposed about the transfer chamber. A substrate may be processed by the cluster tool and transferred between the pre-clean chamber, the SAM deposition chamber, the ALD chamber, and the post-processing chamber. Transfer of the substrate between each of the chambers may be facilitated by the transfer chamber which houses a transfer robot.