A novel automatic biomolecules sorter using thermal gelation of methyl cellulose (MC) solution was realized. In our previous work, we already reported the sol-gel transformation of MC could be used for the flow switch. The flow switch was applied for the prototype of the particles handling system with manual control. The sorting time in this case was about 2 seconds. However the time of sol-gel transformation was estimated within a second. To achieve faster sorting speed, we fabricated a PC controlled sorting system consisting of an automatic fluorescence sample detector, focused IR laser source, and two galvano mirrors for switching and scanning of the laser. As a result the sorting time was reduced to around 100 msec.