I already wrote the author about this, great guy!!, this was his response:
"You can enable/disable sets in settings->sets (path selector combo box). There is also an editbox called select sets which understands all kind of regular expressionss and some variables like %m for manufacturer (see documentation for details). So normally to separate sets you only enable the ones you need (e.g. %m=*namco* for all namco sets) and rebuild them to a new place. Scanner, Rebuilder and Merger will only work on the selected sets then.
Since the region information in MAME is coded within the set description, you might encounter problems. I doubt MAME's setdescriptions are standarized i.e. not all japanese games are called blabla (japan something. You can try to use something like
%d=*(japan* to enable only the ones which got a substring "(japan" in their description. Or if you want to disable japanese sets you can use the "i" button there afterwards to invert the selection. Mulitple selections can be separated by ;.
For example %d=*(japan*;%m=*namco* will only select japanese games made by namco. With regular expressions you can also do something like this:
*[[]b?[]]* enables all sets with a "[b?]" where the ? can be any character. Useful for Cowering's Goodsets
So...play with the settings->sets options....after that, rebuild the selected sets to a new place or whaterver you want to do with them. "
So basically you could separate the roms by regions, but it seems that you would have to delete the duplicates in other languages by hand......