In nanoindentation, the accuracy of obtained data is highly depended on the limitations of the system that the measurements are performed with. In this paper for the first time in the literature, we present a new nanoindentation approach with a system that eliminates the major problems encountered with standard AFM or nanoindentation systems. We present the superior properties of our system and also discuss the current issues with standard systems. The end goal of this research work is to utilize the new approach for accurate mechanical characterization of soft materials which will be used in biological cell mechanics applications.