Page 2: Cleanup and tweak in Photoshop

Here is the texture we exported from Zbrush.

Make a copy of this background layer and turn off the background layer. We will be using Phtotshop to patch up the bake. Use the magic wand tool and select a white area. Select similar. Chances are you have also selected some white highlight areas that we want to leave as is, so subtract those areas from your selection. Then Modify>Expand your selection by about 8 pixels. Delete.

Use the solidify filter from Flaming Pear. This is in their set of free Photoshop filters available for download from their website. I use Solidify B.

You will likely have a few rough edges still. Reselect, expand your selection by 4-8 pixels and feather by the same amount. Then run gaussian blur by about 4 - 12, depending on what looks the smoothest. Any remaining rough spots can be fixed with hand painting or the blur tool. Depending on the shape, you may need to offset and blur seams with the rubber stamp.

Here you have your bake. Depending on how it will be used you may want to adjust levels or contrast and brightness.