We have ever developed the method to realize active path selection of microbubbles at the bifurcation of blood vessel by introducing acoustic radiation force to focus the density. To apply this method to an in vivo experiment, it is necessary to understand the three-dimensional shape of blood vessel and the distribution of bifurcations. Therefore we have developed a method to measure the distribution of bifurcations in blood vessel by positional calibration of the ultrasound probe with the extraction of blood flow in echograms. We used a metal ball marker for calibration. The shape of blood vessels is reconstructed in a graphical interface, where three-dimensional thinning algorithm was applied. This system helps the examiner to adjust the acoustic field for ultrasound therapy using microbubbles.