Lithium niobate (LN) is a widely used artificial optic-electronic crystal. A LN surface is an attractive substrate for the fabrication of photonic crystals (PhCs) in order to form useful optical devices. In this work, two-dimensional microhole lattice arrays with specified structure parameters were fabricated on a LN substrate by means of focused ion beam (FIB) etching. The physical and geometrical reasons for the formation of a nonideal hole shape and the depth limitation are analyzed. The authors have mainly discussed the effect of redeposition and presented equations of depth change tendency and change rate. The influence of the aberration in the hole shape on the PhC's transmission spectrum is also estimated. Insulator enhanced etching is implemented in order to get better quasicolumn holes, and it is partly effective. Their work shows that FIB is a simple way to etch a hole on LN, but it is still necessary to make technical improvements to the process in order to obtain a better hole shape for PhC applications.