A new Monte Carlo (MC) simulator for electron beam lithography process in the multi-layer resists and compound semiconductor substrates has been developed in order to fabricate and develop the high-speed PHEMT devices for millimeter-wave frequencies. For the accurate and efficient calculation of the transferred and deposited energy distribution to the multi-component and multi-layer targets by electron beams, we newly modeled for the multi-layer resists and heterogeneous multi-layer substrates. By this model, the T-shaped gate fabrication process by electron beam lithography in the PHEMT device has been simulated and analyzed. The simulation results are shown along with the SEM observations in the T-gate formation process, which verifies the new model in this paper.