Metal additive manufacturing (AM) technology has been utilized in many industries including automotive, aerospace, and medical. AM Ti6Al4V (Ti64) alloy is highly noticed for production of medical instruments such as dental implants and the machining process is mostly needed during the production or post-processing of these components. Numerical model, as a powerful tool, can be efficiently used for analyzing the machining process. A customized model was employed using a user-written subroutine in this work to evaluate machinability and microstructural changes in cryogenic machining of AM Ti64 alloy. For this purpose, the microstructural changes were simulated as the new numerical outputs. The numerical results of cutting forces, temperature, nano-hardness, and alpha lamellae thickness (grain size) were successfully verified by corresponding experiments from literature. Then, the impact of tool geometry (including rake and clearance angles, cutting edge radius, and nose radius) on the machinability performance was examined. It was found that, the variation of clearance and rake angles were more effective on depth of the hardened layer compared to the other parameters. Thickness of alpha lamellae phase near the machined surface and depth of the affected layer by nano-hardness changes were changed from 0.9 to 1.58 µm, and from 18 to 40 µm, respectively. Overall, it was concluded that the variation of insert positioning made by tool holder (change in rake and clearance angles) was an effective parameter on the process outputs when machining AM Ti64 alloy.