An optical alignment system for aligning a light beam with a core flow in a flow stream. The flow stream may have a sheath fluid and a core flow, where the core flow has a current position within the flow stream. A light source may be used to produce a light beam, and an optical element may be used to direct the light beam at the core flow. In some illustrative embodiments, an actuator is provided for moving the optical element, light source and/or flow stream such that the light directed by the optical element is aligned with the current position of the core flow.