I was wondering if you knew of any mats and wall papers designed with grids or other types of reference lines when doing green screen type stuff in movies?
Also when editing 3D objects is there a freeware software that can merge too objecting into one by overlapping them and telling it to merge them? .STL format preferably.
I haven't seen anything like that. Usually people just use markers, and they don't have to be overly sophisticated either. Take some white gaffe tape and make "+" on your green at intervals a few feet apart, depending on your motion. as long a you have a few of those on the screen at all times, you should be able to track very well and create a virtual 3D camera from your track. I like to put a black circle in the very center of the "+" or outline it with black tape so it is very visible. Just know that you are going to have to roto out these markers in your key. Some people use a color that is close to the background key color, but slightly off so that the tracking program can still pick up the markers.
here are some samples:
With any type of CG compositing, it always helps to really get as many measurements as possible (i.e. distance of camera from backdrop or points, distance between points (if they are uniform), height of camera lens, lens type, etc.) so when you start comping in 3D, you can verify the motion based on your measurments and tracking data.
As far as your second question, the best free tool out there for 3D is Blender. I don't use it, but in looking at its features, I am about to learn it. It handles .stl files, and that would be the first place that I'd look. It has a whole lot of the same functionality as programs like 3DS Max, Maya, and Cinema 4D!