The two-photon cross-linking (TPC) process using ceramic precursors is recognized as a unique fabrication means of real three-dimensional (3D) ceramic microstructures. These structures can be applied to various microscale devices that are used in harsh conditions that demand high strength, high temperature endurance, and good chemical corrosion properties. However, the large shrinkage amount of 3D structures during pyrolysis is a serious limitation to the practical application of these structures; during pyrolysis, asymmetric distortion and shrinkage occur intrinsically. In an attempt to address this, a method is proposed for the precise fabrication of 3D ceramic microstructures that utilize shrinkage guiders to lead to isotropic shrinkage. SiCN ceramic woodpile structures were fabricated to show the efficiency and usefulness of the proposed method. In the results, the woodpiles showed no distortion after pyrolysis.