3D-object breaking through a surface

There is no one layer with one or two effects added solution to the problem you are trying to solve. 

I've got about 40 different approaches that you could take to simulate an actor or a 3D model breaking through a surface. A shot of a 3D dolphin jumping out of a calm ocean would require a different workflow than a robot climbing out of a raging river. They all involve masking or roto or track mattes, position tracking or motion data from keyframes, simulations like particle effects, and at least one layer for each new thing you want to add to the scene. I did something similar a few months ago, and the comp had about 200 layers total in a dozen nested comps (pre-comps). I did something similar a few weeks ago, and the comp had only about 4 layers, including a track matte and some keying. 

Show us a sample image of the completed composite you want to duplicate, or show us your original footage and the 3D object you want to insert into the shot and describe what you want to achieve in detail. We can point you in the right direction.

If you are using Element 3D or Traapcode Effects, check out the plugin developers' website first for tutorials on using their tools. They are almost always the best resource for training.  If you use a 3D app like Blender (free, open source, and incredibly powerful for shots like you are describing) or C4D, a breaking-through-the-surface effect will usually be easier to achieve there. 3D apps are usually the easiest way to simulate water or things breaking apart.

After Effects can be a very good tool to combine those elements into a final, believable shot.