This paper presents the full modeling and a methodology for de-embedding the interferometric scanning microwave microscopy measurements by means of dopant profile calibration. A Si calibration sample with different boron-doping level areas is used to that end. The analysis of the experimentally obtained S11 amplitudes based on the proposed model confirms the validity of the methodology. As a specific finding, changes in the tip radius between new and used tips have been clearly identified, leading to values for the effective tip radius in the range of 45 nm to 85 nm, respectively. Experimental results are also discussed in terms of the effective area concept, taking into consideration details related to the nature of tip-to-sample interaction. The authors wish to acknowledge the support from EC by means of “Marie Curie” fellowship in the framework of PEOPLE-2012-ITN project: Microwave Nanotechnology for Semiconductor and Life Science—NANOMICROWAVE, under GA: 317116, as well as the Region Nord-Pas-de-Calais for supporting this work under the project CPER CIA research and the National Research Agency (ANR) under the program Equipex (EXCELSIOR project).