if the orientation of substrate is not matching with structure of the material. what structure (surface morphology) thin film will show? will it show that of substrate orientation?
Yes. Substrate orientation can significantly affect its surface energy and have a dramatic effect on the resulting film's structure and morphology through the nucleation and growth kinetics (among others).
Just yesterday attended a lecture about this. Check the work of "Toshihiko Tanaka" from Fukushima University. He made an aligned filmed of PTFE and then aligned inks on top.
If the film deposited and the substrate have the same crystal structure then why the question of orientation comes in? For ex: if the substrate is say cubic and is in 111 plane and the film also is cubic then it would take that orientation and which is termed as epitaxy. However if there is small lattice mismatch then the the epitaxy will still work and the film could be understress or strain. If there is a large lattice mismatch then epitaxy will not take place leading to a polycrystalline film. I hope you can build up your answer from these statements.
Let me explain. For epitaxy both the substrate and the film should have the same crystal structure (cubic, hexagonal etc). Now for any given orientation of the substrate the film deposited will take that orientation in preference. If there is a big lattic const mismatch then the film will be polycrystalline. In case of polycristalline films one tcannot take of orientation. Can we? If at the film obtained could be texture. I feel that you are a bot confused or confusing with many issues and not able to ask what exaclyl you need. Sorry.