In this paper, a substrate integrated waveguide (SIW) model has been used to analyze the gate modulation of field effect transistors (FET) with a molecular channel of nanoscale material. By neglecting quantum mechanical effects and by treating nanoscale material as a “rigid” substrate, static electric field distribution inside the FET channel is analyzed. Numerical results show that the modulated electric fields near the interface between the FET channel and the gate insulator vary with dielectric constant of nanoscale material. Moreover, we found that, regardless of channel material and insulator thickness, the electric field penetrating inside the FET channel decreases in a similar way with the distance from the interface. This paper provides useful information for the detailed calculation of I-V curves and for the design of nanoscale FETs.