Because of the everlasting promotion of micro/nano-fabrication techniques, the measurement of the feature contour of micro/nano-fabricated structures become an important issue. Atomic force microscopy (AFM) is a high accuracy measurement instrument that has been frequently used in measuring of micro/nano-fabricated structures. However, most conventional AFM systems use a single probe with a monotonic tilting angle to scan all kinds of sample profiles. This type of AFM design easily suffers from the so-called "side wall effect", and the scanning result will induce a distortion phenomenon at the corner part. To solve this problem, a novel dual probe AFM system is proposed in this paper. A highly flexible system structure is adopted in this work to create different tilting angle of each probe. With the method developed for obtaining the appropriate tilting angle, we set up the so-called "effective tilting angles" under different scanning scenarios. In addition, a useful merging method has been developed to stitch together the scanning results from two different probes out of two different scanning units. For scanning a standard grating, the error of sidewall angle from the scan image decreases form 27.3 % to 4.5 % when our method is compared with a traditional scan. Finally, by integrating the proposed scan method with a new raster based local scan strategy, we can achieve a high-throughput precision scan. In the scan of human blood cells, we not only can remove unnecessary scan area up to 61.04 % but also can improve sidewall distortion. A comprehensive series of experiments have been conducted to validate the scanning capability of the proposed methods on our self-developed AFM system.