Atomic layer processing technology has advanced significantly since semiconductor devices have evolved from 2D to 3D stacked structures. Creating a uniform temperature distribution across the entire wafer during repeated heating and cooling cycles is an important aspect of atomic layer processing. Conventional embedded heaters rely on thermal conduction, resulting in slow heating rates. This can delay the cycle time of atomic layer processes, where rapid temperature changes are crucial. To overcome these problems, this study adopted a method to directly heat the wafer using gigahertz band microwaves. While there has been research on the heating mechanisms and effects of microwave irradiation on Si Wafers, studies on uniformity are lacking. Microwave heating depends on the distribution of the field, thus this study presents methods for improving uniformity by optimizing the antennas and controlling the cavity modes. A 2.45 GHz microwave was propagated in the TE10 mode in a WR-340 waveguide and radiated into the chamber through a slot located on a toroidal antenna designed for uniform heating. The radiated microwaves formed cavity modes within the chamber, thereby heating the 300 mm wafer. The wafer temperature was measured using a fiber Bragg grating sensor array; the heating rate at the top and back of the wafer was 6.5 °C /kW/s, and the within-wafer non-uniformity was 11.68 % and 10.94 %, respectively, after applying 500 W power for 60 s. A comparison of the temperature characteristics of the top and back sides of the wafer indicated no significant differences in uniformity, heating rate, and temperature profile. Based on these findings, it is anticipated that in atomic layer processes, where temperature control is crucial, the proposed method could reduce the process time and increase yield.