The Fermilab Mu2e experiment will search for the neutrinoless coherent muon-to-electron conversion in the field of an Al nucleus. This process violates lepton flavor conservation as stated by the Standard Model and its observation would provide guidance on possible SM extensions. The Mu2e experiment involves intense magnetic fields hence strong magnetic forces, that may lead to misalignments of muon beamline components. The relative misalignment along the vertical axis between the Production Target , the COL3 collimator positioned at the center of the TS, and the Stopping Target can result in several outcomes, such as increased radiation damage of the detectors or additional background events. To address these issues, I have developed a data-driven method to determine the vertical misalignment of the Mu2e beamline. To exploit this procedure, the Mu2e experiment will take dedicated runs. In the case of a vertical misalignment of one or more of the beamline elements, the simulation geometry will be adjusted accordingly. This will allow to tune the simulation to match the data and perform a more reliable estimate of the background sources to the conversion electron search which will be a fundamental task in Mu2e.