Although we have reported our attempts to actively control microbubbles in flow using acoustic radiation force for future drug delivery systems, the microbubbles we used are not applicable for in vivo experiments. Thus, we examined two types of nanobubble with a drug-retaining function. Because the nanobubbles are invisible in a conventional optical observation, we observed the behavior of nanobubbles using ultrasound images (echograms). First, we found the optimal settings of echography to guarantee the relationship between the brightness variation and lipid concentration of nanobubbles. Then, we derived the destructive coefficient using two types of path under continuous ultrasound exposure of 5 MHz. Results indicate that the controllability is related to the construction of nanobubbles and the spatial distribution of the ultrasound field. We realized that the design of the ultrasound field is important with Bubble A, whereas the frequency of ultrasound emission needs to be discussed with Bubble B.