As the measurement scale shrinks, the reliability of nanoscale measurement is even more crucial for a variety of applications, including semiconductor electronics, optical metamaterials, and sensors. Specifically, it is difficult to measure the nanoscale morphology at the exact location though it is required for novel applications based on hybrid nanostructures combined with 2D materials. Here, we introduce an advanced hybrid positioning system to measure the region of interest with enhanced speed and high precision. A 5-axis positioning stage (XYZ, R, gripper) makes it possible to align the sample within a 10-μm field of view (FOV) in both the scanning electron microscope (SEM) and the atomic force microscope (AFM). The reproducibility of the sample position was investigated by comparing marker patterns and denting points between the SEM and AFM, revealing an accuracy of 6.5 ± 2.1 μm for the x-axis and 4.5 ± 1.7 μm for the y-axis after 12 repetitions. By applying a different measurement process according to the characteristics of 2D materials, various information such as height, length, or roughness about MoTe2 rods and MoS2 film was obtained in the same measurement area. As a consequence, overlaid two images can be obtained for detailed information about 2D materials.