Usually, end milling operations have been carried out using conventional uniform helix tools with fixed helix angles. Thus, many studies have been conducted to study the effects of these tools on the thermomechanical properties of a milling process. Recently, there have been works that point to the benefits of using harmonic endmills. Harmonic endmills consist of cutting edge profiles that have continuously harmonically varying helix angles. The variation is described using a harmonic function of axial position (elevation) of points on the cutting edge. In this work, a 3D finite element simulation using ABAQUS, is carried out for the complex milling process of Titanium alloy Ti6Al4V. The envelope of the harmonic tool is first generated using a set of MATLAB codes and stored in a Standard Triangle Language (.stl) format. The machine tool is introduced into an FEM program which has been designed to provide for dynamic effects, thermo‐mechanical coupling, material damage law and the criterion for contact associated with the milling process. A Johnson‐Cook material constitutive equation which combines the effects of strain hardening, strain softening, and temperature softening is used. To account for the chip separation criterion, the Johnson Cook damage evolution equation is used. The milling process simulation for Ti6Al4V is then carried out. In the end, the stress distribution and the cutting forces are obtained.