An auto-aligning system is presented. One embodiment of the auto-aligning system includes a launcher unit configured to direct a first laser beam and a second laser beam through a chamber, wherein the first laser beam is co-linear with the second laser beam. The auto-aligning spectroscopy system further includes a receiver unit configured to receive the first laser beam and the second laser beam passing through the chamber. The receiver unit includes a first detector configured to determine an intensity of the first laser beam. The receiver unit also includes a second detector configured to determine a deviation of the second laser beam from a determined position. Further, the auto-aligning spectroscopy system includes a motorized stage configured to align the launcher unit to a base-line position based on the determined deviation of the second laser beam.