This article deals with a novel hybrid control of an atomic force microscope (AFM) for the robust characterization of interaction tip/sample force regions. The hybrid structure is composed of several position and force controllers and a specific switch compensation structure. A single selected controller is online at a time, and a robust bumpless switch between different control laws is designed. The objectives are the robustness of each controller and switch compensator with respect to uncertain parameters of the AFM. The method uses discrete points in the range of uncertainties. For each operating point, the hybrid controller is designed by an eigenstructure assignment. The method is generalized by a multimodel approach considering only uncertainties defined by a worst-case analysis, thus reducing the conservatism. The order of the controller is related to the number of observers selected by the user. This offers the possibility to design a low-order controller depending on the control specifications. The experimental results demonstrate the effectiveness of the hybrid controller for a fully automated landing procedure of the AFM tip on a sample surface and for force distance curve cycle characterization. Thanks to the robustness of the control method, landing and cycles are reproducible despite actuator uncertainties, friction variation due to aging, and instrumental issues such as the real-time data acquisition.