Abstract: In the MEMS fabrication process of 345 GHz micro-electric vacuum folded waveguide traveling wave tube（FWG-TWT）, the surface roughness and the verticality of waveguides sidewall are two major challenges. Through theoretical analysis and numerical simulation, the paper considered the roughness and studied the changes of FWG slow wave structures performance when the vertical angle tolerance increased from 0 to 6. When the surface roughness of the waveguide became bigger, the signals transmission loss of the slow wave structure increased. When the angles tolerance increased, the signals transmission loss rose, and angle tolerance which means structure change caused the devices operating voltage drift, bandwidth reduction, etc. The results in this paper is helpful for the devices experiment and the processing.