An alignment system (100, 400, 600), comprising: a substrate (105, 405) comprising at least one nanowell (110, 410) and a reflective surface; at least one fluid ejection device (115, 200, 310, 450) configured to be used by a printing device, the at least one fluid ejection device (115, 200, 310, 450) comprising at least one die (120, 315, 415), the at least one die (120, 315, 415) comprising at least one nozzle (125, 320, 420), the at least one nozzle (125, 320, 420) being configured to eject an amount of fluid into the at least one nanowell (110, 410); an alignment device (130, 215, 335) to align the at least one nozzle (125, 320, 420) to the at least one nanowell (110, 410); characterized in that the alignment system (100, 400, 600) comprises: a light source (205, 330, 430) configured to pass light through a surface of the fluid ejection device (115, 200, 310, 450) towards the reflective surface of the substrate (105, 405); and a light sensor (210, 440) positioned on the fluid ejection device (115, 200, 310, 450), wherein the light is configured to be reflected off of the reflective surface and directed to the light sensor (210, 440); and wherein the at least one nozzle (125, 320, 420) of the fluid ejection device (115, 200, 310, 450) is aligned with the at least one nanowell (110, 410) of the substrate if the light sensor (210, 440) receives the reflected light. a substrate (105, 405) comprising at least one nanowell (110, 410) and a reflective surface; at least one fluid ejection device (115, 200, 310, 450) configured to be used by a printing device, the at least one fluid ejection device (115, 200, 310, 450) comprising at least one die (120, 315, 415), the at least one die (120, 315, 415) comprising at least one nozzle (125, 320, 420), the at least one nozzle (125, 320, 420) being configured to eject an amount of fluid into the at least one nanowell (110, 410); an alignment device (130, 215, 335) to align the at least one nozzle (125, 320, 420) to the at least one nanowell (110, 410); characterized in that the alignment system (100, 400, 600) comprises: a light source (205, 330, 430) configured to pass light through a surface of the fluid ejection device (115, 200, 310, 450) towards the reflective surface of the substrate (105, 405); and a light sensor (210, 440) positioned on the fluid ejection device (115, 200, 310, 450), wherein the light is configured to be reflected off of the reflective surface and directed to the light sensor (210, 440); and wherein the at least one nozzle (125, 320, 420) of the fluid ejection device (115, 200, 310, 450) is aligned with the at least one nanowell (110, 410) of the substrate if the light sensor (210, 440) receives the reflected light. a light source (205, 330, 430) configured to pass light through a surface of the fluid ejection device (115, 200, 310, 450) towards the reflective surface of the substrate (105, 405); and a light sensor (210, 440) positioned on the fluid ejection device (115, 200, 310, 450), wherein the light is configured to be reflected off of the reflective surface and directed to the light sensor (210, 440); and wherein the at least one nozzle (125, 320, 420) of the fluid ejection device (115, 200, 310, 450) is aligned with the at least one nanowell (110, 410) of the substrate if the light sensor (210, 440) receives the reflected light.