Two-beam interference ablation of 1,4-Bis(4-methylstyryl)benzene organic crystal by short laser pulses (10 ns, 355 nm) is presented. The influence of laser fluence, interference period, and pulse number on the morphology have been studied. The morphology is closely associated with the molecular interactions in the crystals, and it could be well controlled by adjusting the laser fluence and pulses number. Through interference ablating the crystals with high fluence pulses, and then treated with low fluence laser pulses, grating structures with smooth surface could be fabricated without any additional process.