A sample holder assembly includes a sample tray, a base plate, a stage mount, and a calibration standard mounted onto the stage mount. Three mating structures on the bottom of the base plate mate with corresponding structures on a stage mount that is attached to the sample stage of the SEM. An optional contacting conductor provides electrical contact between the stage mount and the base plate so that charge generated on the sample by the electron beam can leave the sample through the sample conductive layer to the sample tray, to the base plate, to the stage mount, and through the grounded stage.