Thrombus formation is a major consideration and concern in the design and use of implantable biomedical devices including cardiac assist devices and artificial heart valves. To better understand the conditions in which thrombi form and how fluid flows affect the geometry of resulting thrombosis, an in vitro backward facing step model and flow loop is used in combination with magnetic resonance imaging to obtain the geometry of formed thrombi. The simulations are performed with a pulsatile flow to simulate physiological conditions. The imaging is conducted after the flow loop has run for 15 minutes, 30 minutes, 45 minutes, and 60 minutes at a physiologically relevant flow rate to gain an appreciation for the transient development of the thrombus. Post-processing of the magnetic resonance imaging data is performed to create a mesh of the three-dimensional thrombus that will be used for computational fluid dynamic simulations. These studies showed that the thrombi begin to degrade almost immediately during MRI imaging in Phosphate Buffered Saline. The volume was calculated for a thrombus over a 195 minute period and clearly showed a decrease in size. Variations in blood flow time also produced a corresponding change in thrombi size where longer time periods produced larger thrombi.