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Summary: Transmission electron microscope (TEM) specimen preparation by focused ion beam (FIB) milling requires delicate polishing of a thin window of material during the final stages of the procedure. Over or underpolishing is common and requires extra microscope resources to correct. Despite some methods for lamella thickness measurement being available, the majority of users judge the final polishing step subjectively from scanning electron microscope (SEM) images acquired between milling steps. Here we demonstrate successful thickness determination of thin silicon lamellae using calibrated secondary electron detectors in a FIB‐SEM dual‐beam chamber. Unlike previous thickness measurement methods it does not require long acquisition times, the use of in‐chamber scanning transmission electron microscope (STEM) or energy dispersive x‐ray spectroscopy detectors. The calibration aligns a SEM image to an electron energy loss spectroscopy (EELS) map of lamella thickness acquired in a TEM. This calibration reveals the greyscale‐thickness dependence of two secondary electron SEM detectors: the through‐lens detector (TLD) and the in‐chamber electron detector (ICE). It was found that lamella thickness estimation for TLD images is accurate for areas thinner than 0.4 t/λ, whilst ICE images are most accurate for areas thicker than 0.5 t/λ up to 1.1 t/λ. The procedure presented here allows objective lamella thickness determination during the final stages of FIB specimen preparation using conventional imaging modes for common secondary electron detectors. Lay Description: Successful analysis of a material in a transmission electron microscope requires very thin windows of the material to be fabricated. Despite the quality of this analysis relying heavily on the thickness of the window, measuring thickness during window fabrication is not common practice. The authors show that it is possible to measure the thickness of the window directly in a focused‐ion‐beam chamber with a scanning electron microscope without altering the fabrication procedure, and using electron detectors common to most microscopes. [ABSTRACT FROM AUTHOR]