Substrate processing tool with integrated metrology and method of using

A substrate processing method, comprising:

• (a) providing a substrate in a substrate processing tool, the substrate containing an exposed surface of a first material layer and an exposed surface of a second material layer;
• (b) forming a self-assembled monolayer (SAM) on the substrate in a first substrate processing chamber;
• (c) transferring the substrate from the first substrate processing chamber through a substrate transfer chamber to a second substrate processing chamber;
• (d) depositing a film selectively on the first material layer and film nuclei on the self-assembled monolayer in the second substrate processing chamber;
• (e) transferring, after selectively depositing the film on the first material layer, the substrate from the second substrate processing chamber through the substrate transfer chamber to a third substrate processing chamber;
• (f) removing the film nuclei from the self-assembled monolayer by etching in the third substrate processing chamber;
• and
• repeating (b), (c), (d), (e) and (f) sequentially at least once.