Methods are provided, which estimate a quality of a metrology target by calculating a noise metric of its ROI kernels, derived from application of a Fourier filter on the measured kernel with respect to a periodicity of the target's periodic structure(s); and using the calculated noise metric to indicate the target quality. An additional Fourier filter may be applied perpendicularly on the measured kernel with respect to a periodicity of a perpendicular segmentation of the periodic structure(s), and the (2D) noise metric may be derived by application of both Fourier filters. The estimated noise may be analyzed statistically to provide various types of information on the target.