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This paper presents the capability of direct laser writing of complex defect structures in holographically formed three-dimensional photonic crystals in dipentaerythritol penta/hexaacrylate (DPHPA) monomers mixed with photoinitiators. The three-dimensional photonic crystal template was fabricated through prism-based holographic lithography. Defect structures are fabricated through the two-photon polymerization excited by a femtosecond laser. The strengths of two optical lithographic techniques are combined with holographic lithography providing a rapid and large area microfabrication and two-photon lithography providing flexibility in fabrication of defect structures. The optical fabrication process is simplified in the negative tone DPHPA without prebake and postexposure bake as is required of SU-8 while maintaining a capability for constructing photonic structures with small features.