you can use VMD or nanotube modeler

Can these create structures like this? If yes can you please send me some manual which explains this?

Or like this

Or like this?

Nanotube Modeler

http://www.jcrystal.com/products/wincnt/index.htm

Then you can add water with this:

http://www.biomolecular-modeling.com/Products.html

Example:

http://www.biomolecular-modeling.com/Abalone/examples-water-ice-in-nanotubes.html

Alexey Nikitin Thanks. But can nanotube modeller generate nanotube+graphene membrane type of structures as given in above examples posted earlier by me?

Modeller can generate graphene sheets and a lot of nanotubes types.

All the rest we have to do ourself. Abalone has a command for adding a model with the possibility of removal of overlapping molecules. Everything else I would have done with scripts (Abalone has them).

Alexey Nikitin thanks...

try online available generators

Definitively, I would use Mind the Graph. Have you heard about?

It's main advantage is that it is totally online and has a vast library of illustrations of scientific images. Is even better for Pharmacology, Biochemistry, Biology etc

https://www.youtube.com/watch?v=ukJyP5np9fg