A system for separating biological molecules includes a plurality of capillaries (101), a capillary mount (102), a plurality of optical fibers (145a, 145b), a fiber mount (603), an optical detector (138), and a motion stage (606). The plurality of capillaries (101) are configured to separate biological molecules in a sample. Each capillary (101) comprising a detection portion (121) configured to pass electromagnetic radiation into the capillary (101). The plurality of capillaries (101) are coupled to the capillary mount (102) such that the detection portions (121) are fixedly located relative to one another. Each optical fiber (145) includes a receiving end to receive emissions. The optical fibers (145) are coupled to the fiber mount (603) such that the receiving ends of the optical fibers are fixedly located relative to one another. The optical detector (138) is configured to produce an alignment signal. The motion stage (606) is configured to align the receiving ends of the optical fibers (145) to the detection portions (121) based on values of the alignment signal.