I've been editing a lot of ArcView-created maps in Illustrator for the Coastal Bays book. You know how ArcView creates lots of separate objects when you export as an EPS or AI file? For example, the shape for the water is about a dozen separate blue-colored objects. If you select them all, use the "Add to shape area" tool in the Pathfinder palette, then choose Object -> Expand Appearance, it will join together overlapping shapes and make them into one object.
Using the Divide Objects Below (Object -> Path -> Divide objects below) is another great tool - I've been using it to clip the maps to the shape of the Coastal Bays watershed.