Ceramic waveguide components play a critical role in modern microwave semiconductor systems. For the first time, this work reports experimental results obtained when dielectric ceramics are abrasive-machined into waveguide components. This process will cause subsurface damage (SSD), resulting in a deviation in their working frequency which can degrade the performance of the system. For a substrate-integrated waveguide (SIW) resonator working at 10.1 GHz, SSD with a depth of 89 um can cause a maximum frequency offset of 20.2%. For a mm wave component working at 70 GHz, the corresponding frequency offset could increase to 169%. Three resonator SIW filters with SSD are studied, and the results demonstrate that the frequency offset induced by SSD can reduce the pass rate of the filters from 95.4% to 0%. A theoretical analysis is performed to reveal the mechanism and to offer a quantitative estimation of the limiting range of the offset caused by SSD. Feasible methods for reducing the offset caused by SSD, such as structure design, processing optimization, and material reinforcement, are discussed.