The system includes a polishing pad, a pad height sensor; a window; and a window raising mechanism. The polishing pad has an aperture with the window vertically moveable therein. The pad height sensor is positioned above the polishing pad and measures the vertical position of the pad before polishing. The window raising mechanism adjusts the vertical position of the window based on information from the pad height sensor. An endpoint measurement sensor can be disposed beneath the window for in-situ measurement of the polishing process.