The superconducting cavities and, especially, the magnets in high intensity ion linacs need to be aligned to the beam with typical transverse tolerances of±0.25 mm and±0.1 degrees at temperatures of 1.8–4.5 K. This is necessary to limit the emittance growth and minimize the beam losses. A new cryomodule with 7 superconducting quarter-wave resonators and 4 superconducting solenoids has been installed and is now operated at the Argonne Tandem Linear Accelerator System (ATLAS). We developed the techniques necessary to assemble the superconducting components in this cryomodule at room temperature so that they are aligned to the beam axis at 4.5 K. We achieved transverse alignment tolerances of< 0.2 mm RMS. In this paper, we will present the details of the alignment hardware, procedures and results.