Is there a way to select and rotate bones from an imported ogre xml model?

I have looked for a while and I am wanting to understand how to manipulate the bones in an ogre xml animated model manually and from programming.

if i have too i'll get to the vertices and manipulate those, but i was hoping that there are some functions that I could use.

Yes you can. You can disable animation for a particular bone and then control it manually.

Check the test class jmetest.ogrexml.TestTurrentControl for example usage: