1. A system for modifying a three-dimensional model based on one or more anatomical treatment options for a patient, the system comprising: at least one computer system configured for: creating a three-dimensional mesh model representing at least a portion of anatomy based on patient-specific data regarding a geometry of a patient's anatomy including a lumen; determining a geometry of at least one of a plurality of treatment options for treating at least a portion of the patient's anatomy; and modifying the three-dimensional mesh model by deforming an implicitly parameterized surface of the three-dimensional mesh model to simulate insertion of the geometry of the at least one of a plurality of treatment options into the lumen or to simulate removal of the geometry of the at least one of a plurality of treatment options from the lumen of the three-dimensional mesh model.