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In addition to alignment by beam scanning the JEOL 9500 system also has a 2D alignment feature. The working principle of this is that the system will take a SEM image of a specified location and compare the SEM image to a reference image. By comparison of these the system will determine an offset and use this for alignment.

Possible advantages of this is

Alignment can be done using either the Secondary Electron or the Back Scatter detector or a combination of them
Alignment might be possible to features with very low contrast
Alignment can be done to an arbitrary shape

The following will illustrate how to set this up. It is a bit more complicated than regular beam scan alignment and knowledge of beam scan alignment is a prerequisite for understanding the following. Please contact us if you would like to try this alignment mode rather than trying on your own. For reference, the JEOL provided manual for 2D alignment can be found here: File:2D mark detecting 20171212.pdf