Historic building information modeling (HBIM) provides an index frame for digital documentation of the cultural heritage, as a continuous process of reverse engineering. The index frame should be a regular model, with a clear comprehension of each component; consequently, associated knowledge could be live-updated with the investigation progress. Therefore, the method of data registration stresses its importance. The axis is fundamental for Chinese traditional architecture as the basis for positioning all components in wooden structures. However, displacement often happens. To correct the displacement while modeling, the hypothetical axis should be determined first. This paper thus proposes a method of generating the regular axis from irregular column grids and aims to develop an automatic solution that is repeatable and transplantable. The finite element modeling (FEM) abstracts the actual problem to enable numerical calculation. Starting from a candidate solution, the genetic algorithm calculates a solution closest to the expectation from the possible solutions in several minutes. The standard deviation is used to measure the amount of displacement based on the hypothetical axis, which is expected to be minimum. This method is compatible with most kinds of input data, e.g., point cloud, excel data, 2D drawing, mesh model, etc., and applied to a World Heritage Site in Qufu (Shandong, China). The results show the displacement of columns with visual expression and numerical analysis and prove that the proposed method is repeatable and traceable and can easily be applied to different projects by changing input parameters.