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Ultrahigh measurement precision of tunneling current is one of the key requirements in different nanopositioning and scanning systems. The desired precision of tunneling current measurement in vertical direction can be adversely influenced not only because of the sample surface variations and measurement noise, but also because of the cross-coupling while scanning in the horizontal direction. In this paper, few experimental results by considering the vertical system of tunneling current measurement (at ambient atmosphere) with H∞ SISO controller are presented and a comparison is performed with conventionally used classical PI controller. Further, a dynamic modeling of MIMO plant having vertical tunneling current measurement system with horizontal scanning system in the presence of cross-coupling phenomenon is proposed. Then, a robust H∞ MIMO controller is analyzed in simulations in order to achieve the desired measurement precision of the tunneling current.