Method for printing a three-dimensional part layerwise with an additive manufacturing system includes printing layers by depositing material from a print head onto a print foundation, incrementing a position of the print head relative to the print foundation after each layer is printed, and indexing the print foundation carrying the printed layers away from the print head along the printing axis after a number of layers are printed. Printing is performed with driven and fixed rails clamped against movement of the print foundation. Moving the print foundation includes moving the driven rails with respect to the fixed rails in a direction substantially perpendicular to the build plane. Additive manufacturing system includes a drive mechanism to index the print foundation on the printing axis using fixed and driven rails, the driven rails engaging the print foundation for moving the print foundation.