There are several ways to define the non-plated holes in the PCB.
1) You can define certain hole size to be u sed as non-plated holes. For example you can define all 40mil holes in your design to be non-plated, and tell the PCB house you want all 40mil hole to be NPTH
2) You can generate separate NC drill files for NPTH holes.
3) The most professional way is to generate a draw chart as shown in Fig 10.