Use a hone. You can smooth the cylinder wall without removing much material. This You can use a either types of hone. The hone preferred looks like this -
The other hone looks like this -
It will be ideal to use both types of hone's to fix your problem. Begin with the tripod hone to remove the scratch. Complete the process by making a cross-hatched pattern on the cylinder walls with the ball hone. Do this by honing in an up and down motion.
