To establish of standard technique of nano-length measurement in 2D plane, new AFM system has been designed. In the long range (about several tens of ${mu}m$), measurement uncertainty is dominantly affected by the Abbe error of XY scanning stage. No linear stage is perfectly straight; in other words, every scanning stage is subject to tilting, pitch and yaw motion. In this paper, an AFM system with minimum offset of XY sensing is designed. And XY scanning stage is designed to minimize rotation angle because Abbe errors occur through the multiply of offset and rotation angle. To minimize the rotation angle optimal design has performed by maximizing the stiffness ratio of motion direction to the parasitic motion direction of each stage. This paper describes the design scheme of full AFM system, especially about XY stage. Full range of fabricated XY scanner is $100{mu}m imes100{mu}m$. And tilting, pitch and yaw motion are measured by autocollimator to evaluate the performance of XY stage. As a result, XY scanner can have good performance. Using this AFM system, 3um pitch specimen was measured. The uncertainty of total system has been evaluated. X and Y direction performance is different. X-direction measuring performance is better. So to evaluate only ID pitch length, X-direction scanning is preferable. Its expanded uncertainty(k=2) is $sqrt{(3.96)^2+(4.10 imes10^{-5}{ imes}p)^2}$ measured length in nm.