Methods and apparatus to perform wavefront analysis, including phase and amplitude information, and 3D measurements in optical systems, and in particular those based on analyzing the output of an intermediate plane, such as an image plane, of an optical system. Measurement of surface topography in the presence of thin film coatings, or of the individual layers of a multilayered structure is described. Multi-wavelength analysis in combination with phase and amplitude mapping is utilized. Methods of improving phase and surface topography measurements by wavefront propagation and refocusing, using virtual wavefront propagation based on solutions of Maxwell's equations are described. Reduction of coherence noise in optical imaging systems is achieved by such phase manipulation methods, or by methods utilizing a combination of wideband and coherent sources. The methods are applied to Integrated Circuit inspection, to improve overlay measurement techniques, by improving contrast or by 3-D imaging, in single shot imaging.