A surgical system includes methods and systems for damping vibrations. The surgical system can include one or several moveable set-up linkages. A passive, active, or semi-active damper can be connected with one or several of the set-up linkages. The damper can mitigate a vibration arising in one of the set-up linkages and the damper can prevent a vibration arising in one of the linkages from affecting another of the set-up linkages. The active and semi-active dampers can be controlled with a feedback or a feed-forward model. In some embodiments, the system includes a first link supported by a base, a second link, a damper having a variable portion coupling the first link to the second link, and a processor. The processor is configured to detect a movement or a vibration of the second link and adjust the variable portion of the damper based on the detected movement or vibration.