We developed a novel separation method for random screening of target microorganisms from a large heterogeneous population by using a local viscosity control. A thermal sol-gel transformation material is mixed with the sample liquid and we controlled the state from sol to gel and gel to sol reversibly based on the temperature change controlled by heating of the microelectrode with the electric current and focused laser irradiation near the target. The selected microorganisms are fixed on the bottom plate by gel, since the viscosity around the target is temporally increased by the local heating by the focused laser. The other objects are easily washed away by the cleaning flow in the microchamber. Process of fixation, cleaning, isolation and extraction of the target microbe was possible in very short time. Based on this method, two separation systems are developed and basic experimental results of fixation and isolation of targets are shown.