Topological insulators are materials that have an insulating bulk interior while maintaining gapless boundary states against back scattering. Bi2Se3 is a prototypical topological insulator with a Dirac-cone surface state around Γ. Here, we present a controlled methodology to gradually remove Se atoms from the surface Se-Bi-Se-Bi-Se quintuple layers, eventually forming bilayer-Bi on top of the quintuple bulk. Our method allows us to track the topological surface state and confirm its robustness throughout the surface modification. Importantly, we report a relocation of the topological Dirac cone in both real space and momentum space as the top surface layer transitions from quintuple Se-Bi-Se-Bi-Se to bilayer-Bi. Additionally, charge transfer among the different surface layers is identified. Our study provides a precise method to manipulate surface configurations, allowing for the fine-tuning of the topological surface states in Bi2Se3, which represents a significant advancement toward nanoengineering of topological states.