The general objective addresses the challenge of the miniaturized microwave characterization of nanodevices. The method is based on a measurement setup that consists of a vector network analyzer (VNA) connected through coaxial cables to miniaturized homemade coplanar waveguide (CPW) probes (one signal contact and two ground contacts), which are themselves mounted on three-axis piezoelectric nanomanipulators SmarAct™. The device under test (DUT) is positioned on a sample holder equipped also with nanopositioners and a rotation system with μ-degree resolution. The visualization is carried out by a scanning electron microscope (SEM) instead of conventional optics commonly found in usual on-wafer probe stations. This study addresses the challenge related to the control of nanomanipulators in order to ensure precisely the contact between the probe tips and the DUT to be characterized. The DUT is inserted between the central ribbon and the ground planes of the coplanar test structure (width of the central ribbon = 2.3 μm, distance between the central ribbon and the ground planes = 1.8 μm). First, we use classical automatic linear tools to identify the transfer function of a system of three linear nanopositioners along the X, Y, and Z axes. This part allows the precise control of each nanomanipulator using LabVIEW™, with an overshoot of the final value (according to a minimal response time in X and Y) or without an overshoot of the final value (in order to avoid any crashing of the probe tips on the substrate in Z). Second, we propose an angular control methodology (using Matlab™) in order to align the probe tips on the CPW ports of the DUT. Finally, the detection of the points of interest (use of the Harris detector) allows one to determine the set point value of each linear nanopositioner X, Y, and Z. These three steps ensure the precise positioning of the probe tips to ensure accurate microwave characterization of the DUT.