please tell us a litte bit more about your film; e.g. material composition, kind of film production, thickness and procedure of smoothing.....substrate etc.
Now we could only guess and perform a brain storming
And what is your material (and kind of production) and substrate. Only rough description (because it may be a secret).
The thickness isn't that much (less than about 50 atomic distances). What is the value of diameter of your pinholes.
It may be that the beginning of the film growth is characterized by isle growing. The formation to a complete continuous material layer has not yet took place up to the 50th atomic layer. Please see for example the link at the chapter 'growth mode' (Volmer-Weber mode).
I think you should perhaps use an intermediate layer for better adhesion or modify the film processing parameters.
But without more detailed informations all these thoughts are pure speculations.
The roughness of your film is extraordinary (about 2 atomic layers); perfect!
Pin hole formation could be due to different reasons. Here are some of them.
- Thin film being deposited
You have < 10 nm film
- Unclean substrates or unclean environment used for deposition. They could be a dust particle which can stick to the substrates and later on it can disappear leading to the formation of a pin hole.
- If the deposited material is not compatible with your substrate either it is not sticking or there is no lattice matching then that could lead to island formation and can lead to pin hole formation.
- Substrate temperature during deposition. Higher temperatures can lead to annealing and if the film is thin then that can lead to island formation.
As Gerhard Martens pointed out, your layer is very thin and you have to account for the growth model and I doubt that you have a continous layer. Normally PVD films are optical closed layers after you deposit ca. 50 nm of material. You can easily check this by sputtering several thicknesses of layers on glass and looking through it to see the pinholes. With a metallic layer like gold this is easy to check. Mind you that Au can grow differently on glass than it will on Si but you will get some idea. As mentioned by others you can also not exclude particles to be the cause of the pinholes. With such thin layers very small particles (and there are many of them in a vacuum system) can destroy a nice conformal coating. That said, I think the argumentation of the layer growing towards a continous layer is your main problem.