If there are patterns already present on the wafer (as there would be in a more complicated process such as a transistor), this mask must be properly aligned to those patterns.
To do this, the alignment screws are used to move the wafer in the horizontal plane and rotate it about the z-axis until the pattern of this mask properly overlays the existing pattern on the wafer. Blinking arrows in the main window indicate the alignment screw being turned (while the window-in-window view shows what you would see in the microscope).
