A method of generating a three-dimensional model of at least a portion of a heart includes inserting an electrode within the portion of a heart, robotically moving the electrode therein, periodically detecting position information of the electrode to generate a plurality of location points defining a space occupied by the portion of the heart, and generating a three-dimensional model of the portion of the heart including position information for at least some of the plurality of location points within the portion of the heart. The plurality of location points includes at least some location points on the surface of the heart and at least some location points interior thereto. The model is generated by utilizing a surface construction algorithm such as a shrink-wrap algorithm to identify the surface points and isolate or eliminate the interior points.