1. A method of preparing a robotic medical system for use with a shapeable instrument, where the shapeable instrument includes a working end and one or more positioning elements that move the shapeable instrument: obtaining a plurality of localization data to determine a real shape of at least the first portion of the shapeable instrument; pretensioning the shapeable instrument by incrementally actuating at least one of the actuators, thereby causing a movement of the first portion of the shapeable instrument from an initial position to a pretensioned shape, the movement reducing a slack in the shapeable instrument; and providing the movement to a controller including a master input device, wherein the controller accounts for the movement in at least one actuation command where the actuation command manipulates one or more of the positioning elements to reposition the working end or the first portion of the shapeable instrument.