I've created an assembly consisting of 5 flat square parts sandwiched together to make layers (see image).
The way I did it was to create the top part (Layer1) as a part on its own.
I then created a new empty assembly, and inserted the part into that assembly (Assembly tab - Insert Components, browse to the part (Layer1)), and from within that assembly created (Assembly tab - Insert Components - New Part) the next layer down (Layer2) by constraining the outer edges to the edges of Layer1.
Did the same thing for Layer3, constraining the edges to Layer2 and so on.
I then made a circular cut through Layer1 from within the assembly (right click on part, Edit Part).
I then made a cut in Layer2, aligned with the cut in Layer1:
I am able to constrain the centre point of the circle sketch in Layer2 to the centre of the circle sketch of layer 1, cut I can't select any edges or faces of the cut in Layer2 to add a relation to make the circles the same radius. I can however, dimension between the circles, and set the dimension to 0. Why though can I not select the circle of the cut in Layer1 to add a relation between it and the circle of the cut in Layer2?
Is it something to do with Layer1 having been created outside the assembly, then brought into it?
Looking in windows explorer, only Layer1 is visible outside the assembly as a separate file.