Disclosed is a method of measuring a parameter of interest relating to a structure on a substrate, and associated metrology apparatus. The method comprises determining a correction to compensate for the effect of a measurement condition on a measurement signal from a plurality of measurement signals, wherein each of said measurement signals results from a different measurement of the structure performed under a different variation of said measurement condition. The correction is then used in a reconstruction of a mathematical model of said structure to suppress an influence of variations of said measurement condition on the reconstruction.