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, the three-dimensional model representing at least a portion of a plurality of coronary arteries emanating from a portion of the patient's aorta, the three-dimensional model representing at least one fluid flow inlet and at least one fluid flow outlet; create at least one boundary condition model representing fluid flow through at least one of the at least one inlet or the at least one outlet, wherein creating the at least one boundary condition model includes determining an individual resistance for each of the plurality of coronary arteries in the at least one boundary condition model based on a mass or volume of at least a portion of the anatomical structure; determine a first fractional flow reserve within the anatomical structure of the patient based on the three-dimensional model and information regarding a physiological condition of the patient; receive input from a user regarding a plan of treatment relating to a change in the physiological condition of the patient; modify the at least one boundary condition model based on the received input; and determine a second fractional flow reserve within the anatomical structure of the patient based on the at least one modified boundary condition model.