For high precision applications, flexure-based mechanisms have long been popular as they allow highly repeatable motion without problems such as backlash and stiction associated with other motion transfer linkages. In fact, due to the inherent simplicity of flexure mechanisms, these structures have found use in optical alignment, in positioning of cutting tools for high precision machining, as a basis for MEMS structures, and in wafer alignment for photolithography. This thesis discusses the development of a novel monolithic flexure-based structure used for the application of a tool onto a sample. The mechanism is arranged as a nested configuration of two independently moving platforms: the first acts as the reference frame for tool position while the second provides the mount point for the tool. Due to the compliance between the two structures, we obtain a measure of the contact load acting on the tool from the deflection of the two structures relative to each other. However, for the purposes of attaining repeatable positioning, the hysteresis inherent in the piezoelectric actuator used presents a problem. To address this issue, a disturbance observer (DOB) controller is applied in estimating and canceling the hysteresis nonlinearity of the actuator. DOB controllers are conventionally used to compensate against external disturbances. However, in this case, we treat the hysteretic behavior of the actuator as a combination of a bounded hysteresis operator and a linear dynamic system thus treating the hysteresis as a disturbance input to be canceled by the DOB. Experimental results show the effectiveness of the DOB in hysteresis compensation. Finally, we explore the application of this system for depth sensing indentation (DSI). To verify the performance of this system, indentation tests were performed on aluminum samples. The resulting hardness and elastic modulus determined through testing were shown to be close to literature values.