In order for the analysis of data from the tracking detector to reduce the systematic uncertainty on the aμ measurement and improve the sensitivity to a muon electric dipole moment, the internal position of the tracking modules must be known to a high level of precision. Track-based alignment was implemented with data from Run-1 using the Millepede-II framework. An overview of the alignment methods, as well as the verification of alignment with simulation, will be given. A significant improvement in the mean p-value distribution and the fraction of reconstructed tracks after the alignment was achieved. A comparison of the accuracy in the determination of the beam's spatial distribution as a function of time will be presented before and after the alignment.