Systems and methods are provided for indexing a layup mandrel. One embodiment is a method for indexing a layup mandrel for a composite part. The method includes identifying a surface of a layup mandrel that travels in a process direction during fabrication of a composite part, placing a lamination head in contact with the surface, traversing the surface of the layup mandrel with the lamination head, acquiring a stream of 3D coordinates of the lamination head as the lamination head traverses the surface, characterizing the layup mandrel based on the stream of 3D coordinates, altering a Numerical Control (NC) program that directs layup of fiber reinforced material at the layup mandrel, based on a difference between the alignment of the layup mandrel and a nominal alignment of the layup mandrel.