Creating wind in a 3D environment

This problem has been driving me crazy. I am creating a new game using java3D which is loading external models in 3DS format using NCSA Portfolio and Inspector3ds loaders. I don't think you need all that info, but I'm sure someone would have asked if I left it out.

I'm not going to post any code for this question as this is more of a generic problem and doesn't relate to any code I have written yet. I just can't seem to wrap my mind around how to create a wind effect which will blow models clothing around and makes flames flicker. The best I have come up with so far is a completely invisible mesh which would stand up vertically and would travel at a certain speed, anything it hits will move accordingly. This seems like a very complicated solution though and then there's the issue with figuring out which parts of a model are able to be moved by wind.

My game is not so much a game, but a very very small environment which I am creating to explore different possibilities. Expect more questions to follow.