You may need to fashion a block of wood that conforms to the metal roof to spread the pressure of the hammer claw/crow bar base as you pry the nail.
I took two blocks of wood and two pieces of 1/4 steel placed across as short a distance as I could between the blocks. Then resting the hammer on the metal bar pulling the nails.
In my case I had raised over-lapping seams. If you have corrugated roofing that will be harder depending on where they nail it down.