Femtosecond laser pulse directly writing microholes by the matrix microholes ablation technique (MMAT) in a high permittivity microwave ceramic Bi(Nb0.998V0.002)O4 were systematically investigated. The feasible micro-fabricating parameters-output power intensity, writing intervals ΔR and step depth ΔZ, and writing velocity-were discussed and optimized. A large scale crystalline wires array at several hundred nanometers induced by multi-photon absorption was observed and analyzed. The tropism of nanometer array was similar to the epitaxy technique but perpendicular to the writing path. The experiment demonstrated the flexibility and efficiency to micro-fabricated superfine and complex configurations in ceramic materials by femtosecond laser.