Why does the passivation layer in DRIE protect just the mask and not the substrate?

Here's a good link as an introduction to DRIE:  

[BSAC: DRIE Process Development](http://www-bsac.eecs.berkeley.edu/scripts/show_pdf_publication.php?pdfID=1102529945.)  



The $\ce{C4F8}$ (refer Pg. 9 on the link) passivates the entire top layer. But when $\ce{SF6}$ ion bombardment occurs, only the region not covered by the mask is etched. Why does the passivation layer protect just the mask and not the substrate?


Additional reference: [Surface Micromachining Techniques and Materials.](http://www-bsac.eecs.berkeley.edu/projects/ee245/Lectures/lecturepdfs/Lecture3.SurfaceMicromachiningI.pdf)


