Laser pulse duration is a very important parameter to determine the threshold between thermal and nonthermal effects in laser surgery of biomedical tissue. Free Electron Laser (FEL) at Osaka University, Japan, has a pulse structure in which a macropulse (pulse width : 15μs) consists of equally separated micropulses, whose width and interval are ~5ps and 44.8ns, respectively. Precise control of micropulse train may establish fast optic processes because thermal relaxation time in the tissue is about 1us. A pulse-picking system was designed in order to extract single or a few micropulses from an entire macropulse using an acousto-optic modulator (AOM) in which the light path can be temporally diffracted by an external gate signal. An extracted micropulse train was monitored by a mercury-cadmium-telluride (MCT) photodetector with ~1ns response time and recorded on digital oscilloscope. A single micropulse was extracted as a result of adjusting duration of the RF wave to 50 ns which is nearly equal to the interval of micropulse. Investigation of a fast interaction between the FEL and a tissue using this system is expected.