A medical device positioner for use with a remote catheter guidance system (RCGS), which can address angular, lateral and/or translational misalignment of an elongate medical device between the RCGS and an access point on a patients body. The medical device positioner may include a base configured to attach to a remote catheter guidance system, and a first support member extending from the base and having a receiving portion for receiving at least a portion of the elongate medical device.