If there is notable surface material (like piston aluminum), lightly sand it off before you ruin the honing stones. A ball hone will de-glaze the cylinder but if it's got some serious scratches or was just bored, you'll need to use a shoe type hone, about #220 grit stone (if you have a choice).
Be sure to use a cross hatch finish. Hone with WD-40 or another light oil (keep it wet) and run it in and out at a fairly slow rpm, about 600 rpm if possible. Use a slow, rythmic stroke pace, hesitating for a moment at the top and bottom to acheive a 25* to 35* scratch angle for the top and bottom, and a 45* for the center of the bore. Re-install the cylinder with new gaskets and rings and be sure to check the ring gaps (end and side) before putting it togehter. This is how you get the best job for longevity.