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We present microfabricated slow-wave structures for millimeter- or terahertz-wave vacuum electronic sources. A two-level ultra-deep reactive ion etching (u-DRIE) on highly doped silicon wafers has been employed and allowed for complicated 3-dimensional structures with high aspect ratio. The measured spectra of return loss, however, show 1.2% and 6.8% upshifts in both cutoff and resonant frequencies, respectively. We found the suppression of two-level u-DRIE at the narrow channel between resonant cavities has caused the change of aspect ratios, i.e., saddle-shaped bottom surfaces, which is proved to be associated with the difference in frequency shifts as well as RF attenuation by comparison with theoretical prediction.