In vivo visualization systems are described which facilitate tissue treatment by a user in utilizing real time visualized tissue images with generated three-dimensional models of the tissue region of interest, such as the left atrial chamber of a subject's heart. Directional indicators on the visualized tissue as well as the imaging systems may be utilized while other variations may utilize image rotation or manipulation of visualized tissue regions to facilitate catheter control. Moreover, visualized tissue regions may be combined with imaged tissue regions as well as navigational information to further facilitate tissue treatments.