A method and a flow cytometer system in which a light path is aligned to optimally direct light from a light source to a flow cell of a flow cytometer instrument are provided. The flow cytometer may include an orientable mirror disposed in the light path between the light source and the flow cell. By changing an orientation of the mirror through a sequence of different orientations, an optimal orientation of the mirror may be determined, and the mirror may be oriented accordingly before proceeding to conduct a flow cytometry investigation.