let's say we have a perforated plate, due to the computational limit we want to model only flow in one of the holes, how can we use periodic boundary condition,

can cfx do that?

maybe u can use symmetry and not periodic! See Tutorial 8: Supersonic Flow Over a Wing. There u will see the use of symmetry boundary type, at bottom location. But on the half of the hole, you will use Wall as boundary type.