A method for printing a three-dimensional part with an additive manufacturing system, the method including printing layers of the three-dimensional part and of a support structure for the three-dimensional part from multiple print heads or deposition lines, and switching the print heads or deposition line between stand-by modes and operating modes in-between the printing of the layers of the three-dimensional part and the support structure. The method also includes performing a purge operation for each print head or deposition line switched to the operating mode, where the purge operation includes printing a layer of at least one purge tower from the print head or deposition line switched to the operating mode.