Cluster tool with integrated metrology chamber for transparent substrates

The embodiments of the invention relate to a method and apparatus for measuring the etch depth in a semiconductor photomask processing system. In one embodiment, a method for etching a substrate includes etching a transparent substrate in an etch chamber coupled to a vacuum transfer chamber of a processing system, transferring the transparent substrate to a measurement cell coupled to the processing system, and measuring at least one of etch depth or critical dimension using a measurement tool in the measurement cell.