A method for controlling an apparatus to perform a multi-layer chemical mechanical polishing (CMP) process with a polishing rate for a plurality of process runs. For each process run, a multilayered structure with a first thickness formed on a wafer is polished and a second thickness of the multilayered structure is predetermined to be polished away. The method comprises steps of receiving a post-CMP thickness information of the multilayered structure of a first process run, wherein for the first process run, the CMP process is performed for a first CMP process time. Then, a second CMP process time is determined according to the first CMP process time, the first thickness and the post-CMP thickness. Further, the second CMP process time is provided to the apparatus for processing a second process run posterior to the first process run.