A method and system for improving throughput of a fluidic system such as a biopolymer analysis system by cleaning accumulated or clogging biopolymer from the fluidic system is disclosed. The method and system utilize a light energy source to photocleave the biopolymer molecules that may accumulate or aggregate in the fluidic system or clog a passageway. The accumulated biopolymer may be exposed to a light energy source for a sufficient period of time such that the biopolymer molecule is dosed with sufficient energy to photocleave the biopolymer molecules, thereby restoring the efficiency of and flow through the system.