The article presents the features of using the through reactive ion etching of quartz membranes with a thickness of 20 μm or more in the technology of the group manufacturing of pendulums of Q-flex accelerometers. A comparative analysis of the thin-film masking material (aluminum, chromium, titanium, copper, nickel) for the through reactive ion etching of quartz by the selectivity parameters and the temperature stresses introduced into the membrane is carried out. The mechanism of interaction of a copper mask with a fluorine-containing plasma, namely, the formation of copper fluorides on the masking surface and the subsequent increase in the total thickness of the mask with the etching time, are considered. The effect of a local increase in the etching rate of quartz in the region of thermal stresses of the membrane near the masking metal pattern is revealed. To study the effect, a method is developed for decorating a quartz surface with microneedles using an etching mode with an increased bias voltage.