Radio frequency (RF) heating is considered as a potential postharvest technology for disinfesting agricultural products. Heating uniformity is one of the most important problems in practical applications. In this study, three different comparison experiments were conducted to evaluate the heating uniformity in a 6 kW, 27.12 MHz parallel plate RF heating system with a free-running oscillator. The three sample conditions in RF heating experiments include four different thicknesses milled rice placed in the container, the milled rice of 9% and 11% moisture content with 4 cm thickness, and milled rice and soybean with 4 cm thickness and 9% moisture content in the half section of the container. Finally the milled rice sample with low moisture in the corner and high moisture in the center of the container was used to evaluate the heating uniformity improvement. The results showed that the milled rice temperature increased with increasing thickness. Temperatures in corners and edges were higher than those in the center both in RF treated rice and soybeans. The samples of rice or with high moisture were heated more than those of soybean or with low moisture. The RF heating uniformity could be improved by placing the low moisture samples in the corner and high moisture ones in the center. This study should provide useful information for designing practical RF treatment processes as physical disinfesting methods.