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Lithium Niobate has a potential for applications in electronics and communication industries due to its unique electro-optical, piezoelectric and nonlinear properties. Femtosecond laser machining offers the best alternative to machine the mechanically fragile and optically delicate lithium niobate crystal. This paper reports a study of the effect of femtosecond laser machining on the surface integrity of lithium niobate. The transmission electron microscopy reveals a 100nm thin amorphous region and a void. The chemical analysis shows a loss of lithium and oxygen from the surface and sub-surface. Optical illumination facilitates the selective readout of the written spots of 2 microns size.