A system and method for optimizing a fiber optic sensor by properly clocking or rotationally orienting a window with a fiber optic focuser. This method may include shining light through the focuser into the window and receiving with a reflectometer a first reflection from a first surface of the window and a second reflection from a second surface of the window. Next, the method may include calculating a delta of intensities between the first and second reflections, and then rotating an orientation of the window to a next rotational orientation. The steps of rotating the orientation of the window, receiving reflections, and calculating their delta may be repeated any plurality of times to solve for a plurality of deltas. Then, the method may include the steps of determining which one of the deltas is the largest and fixing the window to the focuser at a rotational orientation associated therewith.