In this paper a promising method of recognizing spatial contact state between carbon nanotubes (CNTs) and atomic force microscope (AFM) probe inside scanning electron microscope (SEM) is proposed. The CNTs can be picked up simply and effectively by van der Waals force without knowing depth information of SEM images by using this method. And a micro-nanorobotic manipulation system with 16 DOFs, which allows the automatic pick-up of CNTs based on visual feedback, is presented. The micro-nanorobotic manipulators are assembled into 4 units with 4 DOFs individually. Namely, a manipulator has 4 DOFs i.e., three linear motions and a rotational motion. Manipulators are actuated by picomotors with better than 30 nm linear resolution and less than 1 micro-rad rotary resolution. The van der Waals force mechanics model between CNTs and AFM probe in the picking up manuplation is established. In reality, the van der Waals force is the main attractive force under the vacuum condition inside SEM when the influence of staticelectricity is ignored. It is shown that the van der Waals force under horizontal (sphere-plane) contact model is significantly larger with appropriate overlapping length. Though the positions in both x and y directions of the CNTs and AFM cantilever are acquired, the relative positions of those two objects in the z direction remain unclear. In the gradually ascending process of AFM cantilever to contact the CNTs, the CNTs abruptly drop on the surface of AFM probe due to the van der Waals force. According to the relative coordinate system of SEM visual feedback images, the detection of contact state between carbon nanotubes and AFM probe are completed by using the inclination changing value of fitting line. The experimental results suggest that the abrupt contact between CNTs and AFM probe happens when the inclination changing value of the regression line is found to be 3.0263. The spatial contact state between carbon nanotubes and AFM probe includes line contact (Model a) and point contact (Model b, Model c). Then the dynamic difference method is introduced to identify the spatial contact model of CNTs and AFM probe. The results demonstrate that contact model of CNTs and AFM probe is line contact when the dynamic difference is approximately zero. The position of carbon nanotubes is corrected by moving AFM cantilever automatically underneath the CNTs. The picking-up of CNTs from substrate under line contact model is completed by choosing the optimum contact angle, contact length and pickup speed.