In this work, the study of domain inversion in lithium niobate (z-cut) by electron beam irradiation associated to wet etching, in view to the fabrication of phononic crystals. The inverted domains are revealed by HF-etching taking advantage of the large difference in etching rate between z+ and z- faces. A pertinent choice of irradiation conditions such as accelerating voltage, probe current and injected dose, (parameters of interest for the geometry and size of the obtained domains), was determined and optimized. Two dimensional structures at the micrometer scale were then realized on z-cut LiNbO3. We demonstrate the achievement of 2 to 18 mu m diameter of hexagons, with a very large depth close to 30 mu m, which depends on the etching time. The obtained structures, which exhibit a filling fraction varied from 1% to 64%, were characterized before etching by optical microscopy and by atomic force microscopy to visualize and to characterize the inverted domains. After HF etching, a field emission scanning electron microscopy was used to observe the obtained phononic structures. Taking into account of the obtained filling fraction values and the size of created hexagons, the frequency band gap of these structures is expected at 200-350 MHz range. We have pointed out experimentally the existence of the phononic band gap by combination of phononic crystal with SAWs generation based on z-cut LiNbO3.