@Vignesh_Chakravarthy ALPACA is not a registration tool, and to transfer landmarks from one model to the next. That TPS transform is only approximate and the whole purpose is to provide a fast visualization of where the landmarks will be. See this long thread about it. Increasing ALPACA Non-Rigid Alignment - Support - 3D Slicer Community
If your goal is to do the model registration, use FastModelAlign, however, we don’t currently have deformable registration implemented in it. It is not much work, but we don’t have time or people right now.