We want to make a copy of an organizational structure from one plan variant to another. This copy should include all assignments like purchasing groups to organizational units made in PFOM . Can we do this?

Make sure that the plan number is established through the IMG. (And that it is not the active plan.)
Go Human Resources -> Organizational Management Tools -> Plan version -> Copy.
It runs RHCOPL00. All or any portion of the plan maybe copied and manipulated and then copied back in to the active plan.