A method to locate periodic structures in general three-dimensional Stokes flows with time-periodic boundary conditions is presented and applied to mixing cavity flows. Numerically obtained velocity fields and particle tracking schemes are used to provide displacement and stretching fields. From these the location and identification of periodic points can be derived. The presence or absence of these periodic points allows a judgement on the quality of the mixing process. The technique is general and efficient, and applicable to mixing flows for which no analytical velocity field is available (the case for all three-dimensional flows considered in this paper). Results are presented for three different mixing protocols in a three-dimensional time-periodic cavity flow, serving as an accessible test case for the methods developed. A major result is that periodic lines are obtained for these three-dimensional flows. These lines can be complex in geometry and their nature can change along a line from hyperbolic to elliptic. They can serve as practical criteria in the optimization of three-dimensional mixing processes.