This paper explores the impact of etch holes on sub-terahertz (THz) waveguide transmission performance and presents a silicon micromachined WR-03 waveguide with etch holes. The influence of etch-hole size and grid size is investigated through simulations. The waveguide prototype is realized through deep reactive ion etching (DRIE) and low-temperature thermal-compression bonding. Measurements reveal a low transmission loss (average 0.04 dB/mm) for the etched waveguide, with negligible influence on transmission loss observed for etch hole sizes below a specific threshold, which agrees with the simulations. The findings guide the design and optimization of micromachined THz waveguide components with etch holes applied in some specific situations.