The invention pertains to a reference positioning system for positioning a workpiece in a three-dimensional coordinate system, the reference positioning system comprising a first positioning unit for positioning a first alignment feature of the workpiece in a first dimension, in a second dimension and in a third dimension, comprising a first centring pin and a first reference level locator, a second positioning unit for positioning a second alignment feature of the workpiece in the second dimension and in the third dimension, comprising a second centring pin and a second reference level locator, and a third positioning unit for positioning a third alignment feature of the workpiece in the third dimension, comprising a third reference level locator.