Methods and systems for graphically creating a representation of an anatomical structure, such as a heart, is provided. The distal end of an elongated probe is moved within the anatomical structure, and geometric shapes are defined within a coordinate system. By defining geometric shapes, such as spheres or circles, as the distal probe end is moved within the anatomical structure, the cavity within the anatomical structure can be represented. A representation of at least a portion of the anatomical structure can be graphically generated based on the geometric shapes, e.g., by determining a union of the geometric shapes and conforming the graphical representation around the union of the shapes. In the case of a heart, the union of the shapes will generally represent the blood volume within the heart, so that the graphical anatomical representation (which in this case will be a graphical representation of the endocardial surface of the heart) can be accurately conformed around the representative blood volume.