A method of calibrating an inspection apparatus. Obtaining a surface level measurements (LS) at respective level sensing locations LS(x,y). Determining focus settings (LPA, LPB) for exposure field regions (EFA, EFB) in accordance with surface level measurements (LSA, LSB) having level sensing locations corresponding to the respective exposure field region. Exposing exposure field regions (EFA, EFB) with focus offsets (FO1, FO2) defined with reference to the respective focus settings (LPA, LPB) to produce target patterns at respective target locations. Obtaining focus-dependent property measurements, such as Critical Dimension (CD) and/or side wall angle (SWA) of the target patterns measured using the inspection apparatus; and calibrating the inspection apparatus using the focus-dependent property measurements (CD/SWA) and the respective focus offsets (FO1, FO2). The calibration uses surface level measurements (e.g., LSB(3)) having a level sensing location (e.g., LSLB(3)) corresponding to the respective target location (TLB). Each offset value is thus corrected in the calibration for the local wafer stack unflatness present during exposure.