Auto-focus system and methods for die-to-die inspection

An inspection system for detecting defects in a semiconductor sample having a plurality of identically designed areas, the system comprising at least one memory and at least one processor that are configured to perform the following operations:

• using the inspection system to construct an initial focus trajectory for a first swath of the sample;
• using the inspection system to scan the first swath by following the initial focus trajectory for the first swath while collecting autofocus data;
• generating a z offset measurement vector for each identically designed area in the first swath based on the autofocus data;
• and
• constructing a corrected z offset vector for inspection of the first swath with the inspection tool, wherein 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.