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We report the generation of high energy 2 μm picosecond pulses from a thulium-doped fiber master oscillator power am-plifier system. The all-fiber configuration was realized by a flexible large-mode area photonic crystal fiber (LMA-PCF). The amplifier output is a linearly-polarized 1.5 ns, 100 kHz pulse train with a pulse energy of up to 250 μJ. Pulse com-pression was achieved with (2+2)-pass chirped volume Bragg grating (CVBG) to obtain a 2.8 ps pulse width with a total pulse energy of 46 μJ. The overall system compactness was enabled by the all-fiber amplifier design and the multi-pass CVBG-based compressor. The laser output was then used to demonstrate high-speed direct-writing capability on a tem-perature-sensitive biomaterial to change its topography (i.e. fabricate microchannels, foams and pores). The topograph-ical modifications of biomaterials are known to influence cell behavior and fate which is potentially useful in many cell and tissue engineering applications.