Access a 3D model skeleton programmatically

You're going to need to know what file format blender has saved your model in, then find or write a parser to read that file format and make data structures in memory from it. Then you can write code which manipulates the model and possibly writes the data back to the file. I don't know blender but if it's open source then all the code you need is in there. Otherwise the Ogre project will likely have code to read blenders output. Google for the format name along with "open source" and "parser" to get started.