This article presents the near-field measurement setup and the sensor topology used to measure the backscattered signal from a small spot of $\sim 1$ mm on an FPGA to enable hardware Trojan (HT) detection. The novel sensor topology used in the setup contains a combination of $E$ - and $H$ -field probes with a tip diameter of 0.2 mm, which is used to excite a carrier and receive the modulated scattered signal that carries a signature of the inspected logic circuit. As a proof of concept and to develop insight, an EM-circuit co-simulation is presented to show that the received signal contains a signature of the logic circuit under test, which is imprinted on the relative power levels of the modulated scattered clock harmonics. The received modulated scattering signature was successfully used to detect the presence of an HT in the original circuit with 100% accuracy without false positives. The effects of using $E$ - and $H$ -field probes in very close proximity, such as resolution and mutual coupling, are analyzed and discussed. It is shown that there is a 12% decrease in resolution and less than 0.01 dB impact on invasiveness. The frequency band of operation for the measurement setup is 3–5 GHz. The probe combination is shown to have a spot size of ~1 mm, a coupling isolation better than 20 dB over the whole band and 30 dB for the design frequency.