Maybe this was already answered, but I couldn't find it:
I have a DB schema, where tables have a prefix, to identify them as belonging to a module:
seamgen currently only enable the usage of reveng.xml where you can explicit list the names wanted for tables/columns.
You can patch your version of seam-gen to use a custom reverse engineering strategy if you want finer control over it.
See the docs for hibernate tools on how to do this.