This really should have been asked in the Help for Pepakura thread, since it's a fairly simple question. New threads are really for deep discussions or builds. I am not trying to pick on you, but your very first post sort of goes against forum policy. I do recommend reading the stickies for getting started and such, and maybe writing up an introduction post in the Introduce Yourself thread. We have a bunch of Help!! Stickies at the top of the page which are designed to be places for Q/A, no one expects you to read them, they're just safe places to ask questions that may have been asked before, or are generally simple and not warranting a full discussion.
You can easily break apart 3d models in any mid-level 3d modeling program. I use 3ds Max personally, and it serves me well, but not everyone has access to it. If you are a student or otherwise have access to it, I'd use pro software like 3ds, but it can be very helpful to learn a "free" modeling program like Blender. It will be a bit more difficult to find help on how to use it, and it could potentially be more difficult to do in general, but then you'll always have access to Blender while you may not always get access to pro software.
Generally, you load the OBJ/STL into the modeling program, go into the poly edit mode and select the face/polys that you don't want and delete them! That's the super low-tech way I do, it's fairly simple but it requires you CTRL+Z a lot to save each part of the model. There may be a way to separate them as separate objects within the editor, but I am a bit too lazy to figure that out.
