There are several issues in your settings:
1: in principle, plane wave only works with periodic BCs so the structure has to be periodic. To prevent users using smaller plane wave dimension than the perioid, the software AUTOMATICALLY extends its dimension to be outside of the boundary conditions. This is why it changes.
2: You can use TFSF source as this is a local plane wave. However, the monitor should not touch TFSF as its boundary condition is used for other purpose and the data on the boundary is not physical.
3: If the nano strucutre is finite, the substrate should be infinite in the plane perpendicualr to propagation. Please extend the substrate and all other non-finite size layers to the out side of the PML.
You are navigating away from the AIS Discovery experience