A method and apparatus for in-situ metrology of a workpiece disposed in a vacuum processing chamber. The apparatus may include an optical assembly external to the processing chamber configured to focus a relatively large optical spot over a relatively large working distance to acquire a TE and TM spectra from a periodic array on the workpiece. The workpiece may be disposed in the processing chamber with an arbitrary orientation which is first determined via a reflectance measurement. TE and/or TM spectra may then be acquired by initiating a periodic triggering of a flash lamp based on the determined workpiece orientation to account for variation in placement of the workpiece within the processing chamber. The periodic array from which spectra are collected may be a memory array being fabricated in a semiconductor wafer.