Methods and systems for performing overlay and edge placement errors of device structures based on x-ray diffraction measurement data are presented. Overlay error between different layers of a metrology target is estimated based on the intensity variation within each x-ray diffraction order measured at multiple, different angles of incidence and azimuth angles. The estimation of overlay involves a parameterization of the intensity modulations of common orders such that a low frequency shape modulation is described by a set of basis functions and a high frequency overlay modulation is described by an affine-circular function including a parameter indicative of overlay. In addition to overlay, a shape parameter of the metrology target is estimated based on a fitting analysis of a measurement model to the intensities of the measured diffraction orders. In some examples, the estimation of overlay and the estimation of one or more shape parameter values are performed simultaneously.