The purpose of this work is to develop an input design for the system identification (IDSI) method for improved performance of a 3D position estimation system that uses multiple ultrasonic transducers. In this paper, an input design is proposed based on input/output data gathered from random excitation so as to excite all modes. The data set is then used to compose a new set of input data, from which the system is excited again and identified. The input design method is used for the system identification of ultrasonic sensor pairs (transmitter-receiver) so as to obtain an accurate model. This model is essential for the analysis of the system and its eventual optimization. Results are given that show the comparison of the actual output signal of the system and the output of the model obtained from the IDSI method as well as the identifiability indicator. It is shown that the IDSI is a useful method and improves system identification even in the presence of excessive noise.