1. A system for planning treatment for a patient, the system comprising: at least one computer system configured to: receive patient-specific data regarding a geometry of an anatomical structure of the patient; create a three-dimensional model representing at least a portion of the anatomical structure of the patient based on the patient-specific data; determine a first fractional flow reserve within the anatomical structure of the patient based on the three-dimensional model and a physics-based model relating to the anatomical structure of the patient; modify the three-dimensional model; and determine a second fractional flow reserve within the anatomical structure of the patient based on the modified three-dimensional model.