Systems and method are provided for the elimination/mitigation of vibration arising from a mode transition during a robotic surgery. The robotic surgery can be performed with a patient side cart, portions of which can be affected by the mode transition. Initial parameters for the portions of the patient side cart that can be affected by the mode transition are identified and are used to create a smoothing curve. The smoothing curve can direct the movement of the portions of the patient side cart to transition between the modes. The smoothing curve can be continuously generated until a new mode transition is requested.