Patent Number: 
Section: claims

1. A metrology system comprising:an x-ray illumination source configured to generate an x-ray illumination beam;a specimen stage moveable in a first direction orthogonal to an axis of the x-ray illumination beam and a second direction orthogonal to the axis of the x-ray illumination beam;a specimen moveably attached to the specimen stage;a first occlusion element disposed on the specimen stage adjacent to a specimen, the first occlusion element having a central axis co-planar with the surface of the specimen, wherein the specimen stage in a first position locates the first occlusion element in a path of the x-ray illumination beam such that a portion of the x-ray illumination beam is occluded by the first occlusion element;a second occlusion element disposed on the specimen stage adjacent to the specimen, the second occlusion element having a central axis co-planar with the surface of the specimen and aligned in a direction different from the central axis of the first occlusion element, wherein the specimen stage in a second position locates the second occlusion element in the path of the x-ray illumination beam such that a portion of the x-ray illumination beam is occluded by the second occlusion element;an x-ray detector configured to detect a first amount of transmitted flux at the first position and a second amount of flux at the second position; anda computing system configured to determine a first position of the first occlusion element with respect to the x-ray illumination beam in the first direction based on the first amount of transmitted flux and determine a second position of the the second occlusion element with respect to the x-ray illumination beam in the second direction based on the second amount of transmitted flux. 2. The metrology system of claim 1, wherein the determining of the first and second positions is based on a model of transmitted flux as a function of position of the first and second occlusion elements with respect to the x-ray illumination beam. 3. The metrology system of claim 1, wherein any of the first and second occlusion elements is cylindrically shaped. 4. The metrology system of claim 1, wherein any of the first and second occlusion elements includes a knife edge, wherein the central axis is aligned with the knife edge. 5. The metrology system of claim 1, wherein any of the first and second occlusion elements includes one or more planar surfaces extending in a direction parallel to the central axis. 6. The metrology system of claim 1, further comprising:an alignment camera that generates a first image of at least a portion of the first occlusion element at the first position and a second image of at least a portion of the second occlusion element in at the second position. 7. The metrology system of claim 6, wherein the portion of the first occlusion element includes a first fiducial mark located co-planar with the central axis of the first occlusion element, and wherein the portion of the second occlusion element includes a second fiducial mark located co-planar with the central axis of the second occlusion element. 8. The metrology system of claim 6, wherein the specimen stage moves to a third position with respect to the x-ray illumination beam such that a fiducial mark disposed on the specimen is within the field of view of the alignment camera, and wherein a location of incidence of the x-ray illumination beam on the specimen is determined at the third position based on the first and second images. 9. The metrology system of claim 6, wherein the alignment camera includes an auto-focus mechanism that maintains a sharp image focus by moving a focal plane of the alignment camera by a precisely measured distance, and wherein the alignment camera measures a change in distance between a reference frame and the surface of the specimen at different locations on the surface of the specimen. 10. The metrology system of claim 9, wherein a relative position of the specimen with respect to the first occlusion element in the direction normal to the surface of the specimen is measured based on the autofocus mechanism, and wherein the specimen positioning system moves the specimen in the direction normal to the surface of the specimen such that the relative position is a negligible value. 11. The metrology system of claim 1, further comprising:one or more proximity sensors configured to measure a distance between a reference frame and the surface of the specimen at each of a plurality of different locations on a back side surface of the specimen opposite the surface of the specimen. 12. A metrology system comprising:an x-ray illumination source configured to generate an x-ray illumination beam;a specimen positioning system configured to position a specimen with respect to the x-ray illumination beam such that the x-ray illumination beam is incident on the surface of the specimen at any location on the surface of the specimen and rotate the specimen about an axis of rotation with respect to the x-ray illumination beam such that the x-ray illumination beam is incident on the surface of the specimen at any location at a plurality of angles of incidence;an occlusion element disposed adjacent to the specimen, the occlusion element having a central axis co-planar with the surface of the specimen;an x-ray detector configured to detect an amount of transmitted flux over a range of angular positions of the axis of rotation, wherein at least a portion of the x-ray illumination beam is incident on the occlusion element over the range of angular positions; anda computing system configured to determine an adjustment of a position of the axis of rotation with respect to the x-ray illumination beam based on the detected amount of transmitted flux. 13. The metrology system of claim 12, wherein the computing system is further configured to determine an adjustment of a position of the specimen with respect to the axis of rotation based on the detected amount of transmitted flux. 14. The metrology system of claim 13, wherein the adjustment of position of the axis of rotation and the adjustment of position of the specimen reduce a movement of the occlusion element with respect to the x-ray illumination beam over the range of angular positions. 15. The metrology system of claim 13, wherein the adjustment of the position of the axis of rotation and the adjustment of the position of the specimen are based on a model of transmitted flux as a function of position of the occlusion element with respect to the x-ray illumination beam over the range of angular positions. 16. The metrology system of claim 13, wherein the detecting of the amount of transmitted flux over the range of angular positions and the determining of the adjustment of the position of the axis of rotation and the adjustment of the position of the specimen based on the detected amount of transmitted flux are performed iteratively. 17. The metrology system of claim 12, wherein the x-ray detector is further configured to detect a second amount of transmitted flux over a second range of angular positions of the rotational axis, wherein the x-ray illumination beam is incident on an unpatterned area of the specimen, and wherein the computing system is further configured to determine an offset value associated with the angular position of the rotational axis based on the second amount of detected flux. 18. The metrology system of claim 17, wherein the determining of the offset value involves a fitting of an absorption model to the second amount of detected flux over the second range of angular positions. 19. A method comprising:positioning a diffraction grating disposed on a semiconductor wafer in a path of an x-ray illumination beam at a plurality of angles of incidence at a first azimuth angle and at the plurality of angles of incidence at a second azimuth angle, wherein the first azimuth angle and the second azimuth angle are separated by one hundred and eighty degrees;detecting a diffraction order response signal associated with a measurement of the diffraction grating at the plurality of angles of incidence at both the first azimuth angle and the second azimuth angle; anddetermining an angle of incidence (AOI) offset value between a normal angle of incidence of the x-ray illumination beam relative to the wafer surface and a value of zero angle of incidence as measured by a wafer positioning system that positions the diffraction grating in the path of the x-ray illumination beam, wherein the AOI offset value is the value of angle of incidence measured by the wafer positioning system at a point of symmetry associated with an intersection of the detected diffraction order response signal associated with the first azimuth angle and the second azimuth angle. 20. The method of claim 19, wherein the diffraction grating includes a periodic structure oriented at an oblique angle with respect to a surface of the semiconductor wafer. 21. The method of claim 20, further comprising:determining a value of the oblique angle as a difference between a first value of angle of incidence measured by the wafer positioning system associated with a peak value of the detected diffraction order response signal associated with either the first azimuth angle or the second azimuth angle and a second value of angle of incidence measured by the wafer positioning system associated with the point of symmetry. 22. The method of claim 19, wherein the diffraction order response signal includes signal information associated with multiple diffraction orders.