What effect are you using?
I don't use Element 3D so I am not sure what's going on there. I also do not know what you are trying to accomplish. Usually when things are not working your workflow is incorrect. I would suggest digging through Video Copilot's tutorials and their forum for help. Make sure you carefully explain what you are trying to accomplish and how you got to where you are.
If you want to apply another deformation effect to the layer then just pre-compose it and apply any of the distort effects you find under Effect>Distort