Not sure what Canon printer you have but for my Pro 100s there's an option in the driver in: Maintenance > Custom Setting > Check box for Prevent Paper Abrasion.
This raises the print head up slightly so it's less likely to touch the paper. It doesn't make any noticeable difference to the print quality.
You could also try placing something on the output tray to keep the paper level as it comes out. I've found with mine that as the final part of the print is taking place, as the front of the paper sags leaving the printer, it was causing the back end to raise slightly and get smudges (sometimes). I use an A4 large letter cardboard box on the output tray to keep the paper level as it comes out and this generally solves the problem,