The pieces at the top of the windshield, and the top and bottom of the rear window are aluminum core with an EPDM rubber co-extruded skin. The skin gives the part it's cross-sectional shape. You CAN remove the rubber, but you'll only have the aluminum core, which doesn't have the same shape. I think it will leave large gaps between the body and glass. These parts can be purchased new from Ford. They run about $55.00 each.
The roof side pieces are aluminum also, but they are painted. You should be able to scuff and re-shoot these parts. The front sections are riveted to the body in 9 places each. These will need to be drilled out for removal. The rear sections can be gently pryed out of the body slot, but there is a nut that needs to be removed first from inside the car. You can see a small round plug near the roof on the rear side panels inside. Pop those out and unwind the nut. The side rails are no longer available from Ford.
Good Luck,
JD