Surface-enhanced Raman scattering (SERS) fiber probes are useful for remote and online detection of harmful molecules using the SERS effect. In this study, a 3-dimensional (3D) SERS optical fiber probe is proposed. The formation of the 3D optical fiber probe mainly included three steps: construction of monolayer polystyrene (PS) spheres as a mask on the end face of the fiber, reactive ion etching (RIE) for PS spheres and fibers, and metal sputtering deposition. Compared with flat surface fiber probes, these 3D SERS fiber probes are composed of ordered nanocolumn arrays, which have the advantages of a simple manufacturing process, low cost, high sensitivity, and good stability. The structures of the 3D SERS fiber probe can be well controlled by changing the size of the PS sphere and etching time. The formation of the nanocolumn was studied using time evolution experiments. The obtained fiber SERS probe has good stability and high sensitivity for the in situ detection of 4-aminothiophenol (4-ATP) in solution. Therefore, these 3D SERS fiber probes have potential applications in harmful molecules for real-time detection.