Micro-cantilever based devices have revolutionized imaging and they are the primary tools for investigation and control of matter at the nanoscale. In certain applications like single electron spin detection, it is essential to maintain a sub-nanometer tip-sample separation for extended periods of time. The existing techniques of atomic force microscope (AFM) operation are not suited for such applications. In this paper a novel approach based on the thermal noise response of the cantilever is developed that promises to meet the aforementioned challenges. The presented technique exploits the dependence of the tip-sample separation and cantilever's resonant frequency to maintain a small tip-sample separation by regulating the effective resonant frequency. The resonant frequency is estimated from cantilever's response to the thermal noise forcing. The experiments performed in ambient room conditions have achieved tip-sample separations as small as 1.5 nm for time periods in excess of 30 min.