Printing Machine Stock Removal Arms

OK, Any makers out there that can help me. I am adding pneumatic tubes inside this part (The magenta in the wireframe), and when printing they are filling in what I suspect to be support material. I am using Simplify 3D which is awesome for scaling and such, just cannot figure out how to keep those tubes hollow.

Made these guys to replace some PVC items that are on our machine that kept breaking. So far so good. Note: The originals work well, but I am embellishing with a pneumatic lifting