without seeing the part.
a) Peel just the area you need. Start peeling on the edge and then use scissors or xacto knife or a safe cutter
to cut away the area making sure not to scratch the part. Then find a protective film to cover the exposed area.
b) Peel off the whole protective soil. Apply logo and then apply new protective foil/film/sheet. Google 3M or protective sheets/films
Have you talked to your vacuum former for suggestions? This is a typical second operation so they should have a process to protect the parts before shipping.
Good luck.