Well some time ago I posted a question on here about motion capture and someone linked me to a site full of motion capture files but I have a problem. The only format I see which is compatible with blender is the C3D format but when I import it the animation keys are not standard and so they are not compatible with my model exporter. I tried to step through the animation and key the frames manually but that didn't work, for some reason the way it is animated there is no rotation to key. I don't understand this type of animation, how can I convert it to standard key frames?

Your question is far from clear.
Please provide step by step screenshots of what you are doing, what your mocap data and your model look like, and what exactly is "not standard" and "not compatible".