Rattlehead15 essentially explained the purpose of alignment briefly and quite well.
Raw HSC exam marks are first determined (i.e. the actual marks that students received for their HSC exams with no changes of any kind) and then aligned, resulting in aligned HSC exam marks, which contribute 50% of HSC marks. As part of your HSC results, NESA informs you of your aligned HSC exam marks (the name for which being Examination Mark).
With that being said, keep in mind that alignment has no effect on a student's ATAR.