Technologies for soft tissue analysis are advancing at a rapid place. For instance, elastography, which provides soft tissue strain images, is starting to be tried in clinical practice as a tool for diagnosing cancer. Soft tissue deformation modeling and analysis is also an active area of research that has application in surgery planning and treatment. Typically, quantitative soft tissue analysis uses nominal values of soft tissue biomechanical properties. However, in practice, soft tissue properties can vary significantly between individuals. Hence, for soft tissue methodologies to reach their full potential as patient-specific techniques, there is a need to develop ways to efficiently measure soft tissue mechanical properties in vivo. This paper describes a prototype real-time ultrasound (US) indentation test system developed to meet this need. The system is based on the integration of a force sensor and an optical tracking system with a commercial US machine integrated with a suite of analysis methodologies. In a study on a single-layer phantom, we used the system to compare various methods of estimating linear elastic properties (via a theoretical approximation, 2-D finite element analysis, 3-D finite element analysis and a standard material-testing method). In a second study on a three-layer gelatin phantom, we describe a new finite-element-based inverse solution for recovering the Young's moduli of each layer to show how the system can estimate properties of internal components of soft tissue. Finally, we show how the system can be used to derive a modified quasilinear viscoelastic (QVL) model on real breast tissue.