A surface analysis scanner system includes calibration targets, which include a target substrate and a film covering the surface of the target substrate which is scanned by the surface scanner. The film is antireflective to the particular scanned light. Particles which contaminate the antireflectance film on the substrate do not scatter sufficient light to be detected by the surface analysis scanner detectors and thus do not interfere with the calibration of the scanner. The calibration targets may include reference features which are etched into the substrate surface or deposited on the antireflectance coated substrate surface which scatter light in a manner similar to particles on a surface. The reference features may also be imbedded in a transparent material supported by the antireflectance coated substrate with a second antireflectance film coating the upper surface of the transparent material. A surface analysis scanner system may also include a support structure for supporting an object to be scanned, an aperture structure, and a light trap structure for blocking the scanned light. Each structure includes a substrate having a coating of antireflectance film. A surface analysis scanner system may also include methods, utilizing antireflectance films, for reducing the amount of scanned light scattered by particles on a scanner system surface.