You can order them, at least the trunk mat (the part that sits on the plastic base to keep stuff from sliding around/protects the plastic) - from online shops like
http://trdparts4u.com and
http://www.1sttoyotaparts.com.
I was able to have my local dealership get me a mat and price match those online dealerships - since both sites have physical dealerships attached to them.
The part that spans the top, think they call it a cargo cover. I've only been able to find ones for the FJ Cruiser and the Sequoia - I know they make them for the Matrix as they were in the original sales brochure (but I didn't remember seeing a part number for it).
Some people were able to build their own cargo cover - using the 4 D-rings on the sides and the two channel rails to support a piece of plywood, cut to match the interior dimensions and supported by hooks on the bottom (attaching to the D-rings and ring for channel rails on the back of the rear seats). Then covered the whole works with automotive carpet to give it that OEM look.