To remove an individual student from an assessment markbook, go to: Admin > Classes.
Scroll down to find the class you wish to remove the student from.
Click onto the black cog next to this class.
Click onto the red x next to the student you wish to remove.
Alternatively if you have many classes you wish to remove the student from please go to: Admin > Classes > Add Students to Class - select the year group and form of the student (this will show all students in that year/form and all of their classes assigned to them) - find the student and click the red cross for each class you wish to remove them from.