A computer-implemented method of identifying and modeling unresolved vessels, and the effects thereof, in image-based patient-specific hemodynamic models, the method comprising: receiving, in an electronic storage medium, one or more patient-specific anatomical models representing at least a vessel of a patient; determining from the one or more patient-specific anatomical models, using a processor, the values and characteristics of one or more patient-specific morphometric features; determining values or characteristics of one or more unresolved or unmodeled vessels in the one or more patient-specific anatomical models, based on a discrepancy between the patient-specific morphometric features and the values and characteristics of one or more reference morphometric features corresponding with the one or more patient-specific morphometric features, said values or characteristics of one or more unresolved or unmodeled vessels including at least one of: a presence or a location of unresolved or unmodeled vascular branches in the vascular model; a quantity of unresolved or unmodeled vascular branches at each location in the vascular model; a length, diameter, or size of the unresolved or unmodeled vascular branches at each location in the vascular model; and an effect of the unresolved or unmodeled vascular segments on the fluid dynamics of blood flow; modifying the one or more patient-specific anatomical models using the determined values or characteristics of the one or more unresolved or unmodeled vessels; determining a blood flow characteristic of the patient using the one or more modified patient-specific anatomical models, said blood flow characteristic comprising at least one of: a fractional flow reserve value, a blood flow magnitude, rate or direction, a perfusion characteristic, a pressure value, a blood flow velocity, or a combination thereof, or transmission of a contrast agent or drug, coronary wall stress, organ perfusion, or coronary flow reserve; and outputting one or more of the determined blood flow characteristic or a hemodynamic simulation using the determined blood flow characteristic to an electronic storage medium or display. receiving, in an electronic storage medium, one or more patient-specific anatomical models representing at least a vessel of a patient; determining from the one or more patient-specific anatomical models, using a processor, the values and characteristics of one or more patient-specific morphometric features; determining values or characteristics of one or more unresolved or unmodeled vessels in the one or more patient-specific anatomical models, based on a discrepancy between the patient-specific morphometric features and the values and characteristics of one or more reference morphometric features corresponding with the one or more patient-specific morphometric features, said values or characteristics of one or more unresolved or unmodeled vessels including at least one of: a presence or a location of unresolved or unmodeled vascular branches in the vascular model; a quantity of unresolved or unmodeled vascular branches at each location in the vascular model; a length, diameter, or size of the unresolved or unmodeled vascular branches at each location in the vascular model; and an effect of the unresolved or unmodeled vascular segments on the fluid dynamics of blood flow; modifying the one or more patient-specific anatomical models using the determined values or characteristics of the one or more unresolved or unmodeled vessels; determining a blood flow characteristic of the patient using the one or more modified patient-specific anatomical models, said blood flow characteristic comprising at least one of: a fractional flow reserve value, a blood flow magnitude, rate or direction, a perfusion characteristic, a pressure value, a blood flow velocity, or a combination thereof, or transmission of a contrast agent or drug, coronary wall stress, organ perfusion, or coronary flow reserve; and outputting one or more of the determined blood flow characteristic or a hemodynamic simulation using the determined blood flow characteristic to an electronic storage medium or display. a presence or a location of unresolved or unmodeled vascular branches in the vascular model; a quantity of unresolved or unmodeled vascular branches at each location in the vascular model; a length, diameter, or size of the unresolved or unmodeled vascular branches at each location in the vascular model; and an effect of the unresolved or unmodeled vascular segments on the fluid dynamics of blood flow; modifying the one or more patient-specific anatomical models using the determined values or characteristics of the one or more unresolved or unmodeled vessels; determining a blood flow characteristic of the patient using the one or more modified patient-specific anatomical models, said blood flow characteristic comprising at least one of: a fractional flow reserve value, a blood flow magnitude, rate or direction, a perfusion characteristic, a pressure value, a blood flow velocity, or a combination thereof, or transmission of a contrast agent or drug, coronary wall stress, organ perfusion, or coronary flow reserve; and outputting one or more of the determined blood flow characteristic or a hemodynamic simulation using the determined blood flow characteristic to an electronic storage medium or display.