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I need to fill the area outside the flow channels and the pillars, leaving the area between the pillars and the flow channels not filled.

Thanks for your question and sending a sample DXF.

The DXF is built with "hierarchy" and those holes are within an inserted block. Blocks contain nested data that references other objects (it's not real objects that ACE can apply fill rules).   This means blocks must be exploded to permit DeEmbed fill to occur.  Simply select all blocks in AutoCAD and use command "Explode".  Save the DWG and convert using ACE.

For ACE to perform FILL requires the following:
* Entities must exist on the same layer.
* Entities mush have the same "Hierarchy Level" (i.e. inside the same block). 

Here's a somewhat similar situation in our user forum for a customer who works with GDSII:
http://forums.numericalinnovations.com/post/not-all-gds-layers-show-when-i-go-to-build-my-composite-7398213
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