We demonstrate versatility of femtosecond direct laser writing (DLW) technique for microstructuring of iron-doped and as-grown lithium niobate crystals. Formation of extended, metastable, and re-writable refractive index modulation structures is achievable via fast local photorefractive modification of refractive index at the focus of the writing laser beam, with a modulation of up to ∆n ~ 10-3, without permanent structural damage to the host crystal. Non-destructive photomodification allows total or partial erasure or modification of the previously recorded structures. This capability may enable realization of optically reconfigurable diffractive optical elements in the same volume of lithium niobate crystal. Flexibility of the DLW technique can be exploited for threedimensional microstructuring of periodic and aperiodic patterns with controllable index modulation profiles.