Disclosed are methods and apparatus for detecting defects in a semiconductor sample having a plurality of identically designed areas. An inspection tool is used to construct an initial focus trajectory for a first swath of the sample. The inspection tool is then used to scan the first swath by following the initial focus trajectory for the first swath while collecting autofocus data. A z offset measurement vector for each identically designed area in the first swath is generated based on the autofocus data. A corrected z offset vector is constructed for inspection of the first swath with the inspection tool. Constructing the corrected z offset vector is based on combining the z offset measurement vectors for two or more of the identically designed areas in the first swath so that the corrected z offset vector specifies a same z offset for each set of same positions in the two or more identically designed areas.