hiding files from emplode/jemplode

Is there a way to hide files from either emplode/Jempeg so that I can maintain my computer to empeg directory structure while not copying over certain directories? I would rather not change my computer directory structure, and I like being able to sync by just dragging all my directories.

Jemplode will ignore any files beginning with a period so you could rename directories you don't want to sync to begin with a period. It seems like a better long term solution would be to rearrange your directory structure though.

-Mike