Disturbance compensation in computer-assisted devices include a first articulated arm configured to support an imaging device a second articulated arm configured to support an end effector, and a control unit coupled to the first articulated arm and the second articulated arm. The control unit is configured to set a first reference frame, where the first reference frame is based on a first position of the imaging device at a first time. The control unit is further configured to detect a first disturbance to the first articulated arm moving the imaging device away from the first position, receive a command to move the end effector, and transform the command to move the end effector from a command in the first reference frame to a command in a reference frame for the end effector.