The scanning microwave microscope (SMM) has been proven to be a useful metrology tool for semiconductor characterization and biological imaging. The raster scan controlled by the feedback of force as in an atomic force microscopy (AFM) affords SMM nanometer vertical resolution and sub-micrometer lateral resolution. The microwave signal injected through the SMM probe allows it to analyze the electromagnetic properties of the sample from the reflected signal. The microwave signal penetrates into the sample on the order of micrometer to characterize layers below the surface.The SMM raw data is convoluted with the sample topography, making it especially challenging for quantitative characterization of nonplanar structures. Using the topography information simultaneously obtained by the AFM and the in situ extracted probe geometry, we de-embed from the topography-corrupted SMM data the sheet resistance of 2D electron or hole gas (2DEG or 2DHG) buried at the interface of an AlN/GaN heterostructure, including the lateral depletion of the 2DEG from an etched step. The SMM results are validated by Hall-effect measurements. The limitation and possible improvement of the present technique are discussed. With improved setup, the SMM can be used to nondestructively monitor the local sheet resistance of 2DEG or 2DHG during device manufacture. These studies help pave the way to 3D microwave tomography on the nanometer scale. In addition to the materials characterization, the transfer characteristics of the HEMT are characterized by traditional SMM. A new analytical circuit model is proposed to illustrate the probe-sample interactive admittance in good agreement with finite-element simulations. The extracted Gsh decreases from 3.2 × 10-4 S∙sq at 0 V to 1.6 × 10-6 S∙sq at -8 V. The on/off ratio is approximately 200, while the DC probed on/off ratio is about 103. The discrepancy is highly possibly due to the weaker gate controlling of the SMM probe compared to the typical gate finger. The defects in 2DEG exhibits inhomogeneities in transfer characteristics, resulting in 1 V discrepancy in threshold voltage and degradation in transconductance. Recently, an inverted SMM (iSMM) has been developed to improve the dynamic range, bandwidth, and robustness of SMM [6]. The improvements by the iSMM have been shown in characterization of biological cells and 2D atomic layers. Unlike conventional SMM, the iSMM allows 2-port measurements in which the SMM probe is grounded while scanning over a sample mounted on a transmission line with its input and output connected to Port 1 and Port 2, respectively, of a vector network analyzer (VNA). To evaluate the possibility of further improvement to 3-port measurements, in this paper, the iSMM probe is connected to Port 1 of the VNA while scanning over an ungated GaN/AlN high-electron-mobility transistor (HEMT). The drain remains connected to Port 2. To modulate the HEMT channel, in lieu of an actual gate, a DC bias is superimposed on the iSMM probe as in conventional SMM.