An electrophoresis apparatus includes a multi-capillary array having a liquid or solid disposed between the capillaries of the array. The liquid or solid exhibits a refractive index higher than that of air and less than that of water and reduces the amount of laser beams scattered by the capillaries. Also provided are methods of adjusting refracted and reflected excitation light beams passing through capillaries of a multi-capillary array, to reduce loss of intensity of the laser beams and increase irradiation of respective samples disposed in the capillaries.