The targets of therapeutic ultrasound are often located behind strongly scattering objects and layered tissue. These inhomogeneities can degrade the intended foci and misdirect acoustic energy causing unwanted hot spots or failure to meet the therapeutic endpoint at the target. We have previously shown the capabilities of dual-mode ultrasound arrays (DMUAs) in imaging strongly scattering objects in the path of the HIFU beam and, consequently, refocusing the beam to optimize the power deposition at the target while minimizing direct exposure to the obstacles. This capability may be a key to successful transthoracic targeting of abdominal tumors. We have experimentally verified the efficacy of this approach in improving the quality of the therapeutic focus and minimizing collateral damage to critical tissue structures in the path of the HIFU beam. In order to study the phenomena associated with transthoracic focusing more thoroughly, we have developed a finite-difference time-domain simulation capable of characterizing the transient propagation of the therapeutic beam through inhomogeneous, attenuating media. This simulation is shown to provide the necessary information for aberration correction of deep seated foci as well as control over the acoustic field at select points. In addition, the FDTD simulation allows for computation of the temperature rise throughout the therapeutic region as governed by the transient bioheat transfer equation. We have validated the predictive abilities of our simulation with hydrophone measurements as well as thermocouple readings from within tissue mimicking phantoms. The experimental validation of the simulation model allows for its use as a key component in treatment planning of thermal therapy using HIFU. Experimental and simulation results demonstrating the role of the advantages of incorporation of the computational model in optimizing the quality of HIFU beams will be presented and discussed.