The 3 SEM Alignments:
Focusing moves the smallest part of the electron probe to the sample surface for finer detailed images.
Aperture alignment centers the aperture around the beam for more consistent focus.
Stigmator alignment yields a circular cross-section of the probe for the sharpest image when focused.
When starting imaging, complete each alignment in order. You will make small adjustments to the focus to help with the other alignments.
Once the SEM is aligned, you should need only small adjustments unless some beam settings are changed, such as the accelerating voltage and probe current or spot size.