Systems and methods are provided to aid in planning at least a portion of a total knee arthroplasty procedure. The system and method automatically aligns the implant components and the bones according to a desired clinical alignment goal with minimum user input. The system and method further allows the user to adjust the position and orientation of the femur, tibia, or implant in a clinical direction regardless of a pre-adjusted position and orientation of the femur, tibia, or implant. The graphical user interface is provided that includes a three- dimensional (3-D) view window, a view options window, a patient information window, an implant family window, a workflow-specific tasks window, and a limb and knee alignment measures window.
