A system and method of aligning with a reference target includes a computer-assisted medical device. The computer-assisted medical device includes an orientation platform, one or more first joints proximal to the orientation platform, one or more second joints distal to the orientation platform, one or more links distal to the orientation platform, a reference instrument coupled to the orientation platform by the second joints and the links; and a control unit coupled to the first joints and the second joints. The control unit determines a pose of the reference instrument. The pose includes a reference point and a reference orientation. The control unit further positions the orientation platform over the reference point using the first joints, rotates the orientation platform to align the orientation platform with the reference orientation using the first joints, and maintains the pose of the reference instrument using the second joints.