With the constant improvement of micro-fabrication techniques, the measurement of feature size of micro-fabricated structures becomes an important issue. Atomic force microscopy (AFM) is a high accuracy measurement instrument which has been widely used in micro-fabricated structures measurement recently. However, due to the monotonic tilting angle of the probe in traditional AFM system, the scanning results of sample with high steep wall feature usually have distortion phenomenon at the corner part of the sample. To solve this problem, a novel dual probe AFM system is proposed in this paper. A system structure with high flexibility is used in this work to create different tilting angle of each probe. With the tilting angle deciding method developed in this paper, we can estimate the effective tilting angles for scanning under different scenarios. In addition, a useful merging method is also designed in this work, which can stich result from different scanning unit together and produce high-precision scanning results. Experimental results are shown to validate the outstanding capability of the proposed system and methods.