Friction Stir Welding (FSW) is a solid-state joining process where workpieces are welded together using a non-consumable pin-tool that rotates and moves along the interface. The joining occurs due to heat generated by plastic deformation and friction between the tool and the material. Simulating FSW processes is a valuable tool for predicting material flow, temperature distributions, tool reaction forces, metallurgy, and potential weld defects. The goal is to assist industrial applicants in optimizing process parameters and producing higher-quality welds. FSW is a highly coupled, thermo-mechanical problem, typically modeled as a fluid mechanics problem. Due to non-axial symmetric tool shapes, an Arbitrary Lagrangian-Eulerian (ALE) framework is mandatory, resulting in frequent re-meshing. The presented approach [1] addresses this issue by modeling the tool-workpiece interface using CutFEM. This leads to a structured, non-body-fitted mesh with undeformed elements, allowing for arbitrary tool geometries and movement. Orthogonal Subgrid-Scales are used to address instabilities due to incompressible material behavior and the convection-dominated nature of the thermal problem. The Ghost Penalty method is used to address small cut instabilities. The developed FE framework directly reads and processes CAD files (STEP/IGES/STL) of pin-tools and computes a discrete level-set function, on which the CutFEM algorithm is based. Consequently, pre-processing efforts are greatly reduced, especially when frequently modifying tool geometries. The resulting temperature evolution curves and reaction forces are in good agreement with experimental data. The developed framework is used to study the influence of welding parameters and tool shapes, including concave and featured shoulders and threaded and fluted pins. [1] H. Venghaus, M. Chiumenti, J. Baiges, D. Juhre, and N. Dialami, Embedded technology for enhanced modeling of Friction Stir Welding processes. Computer Methods in Applied Mechanics and Engineering, Vol. 435, pp. 117539, Feb 2025.