Hi Mike,
You can simply use metadata as part of your file and folder structure. There is an "M" button that opens up a tree of metadata fields. Simply insert elements of your file's source path to preserve your original file/folder structure (or create a new one).
For example
{PathElement.2}/{PathElement.1}/{PathElement.0}
Will create files in subfolders using the original file and two subfolder names, for example.
More info on the old IRIDAS help page at:
http://doc.iridas.com/index.php/Advanced_Output_File_Name_Specification_for...
Hope this helps,
Lin
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Lin Sebastian Kayser - Adobe SpeedGrade Engineering Director - Founder of IRIDAS
