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Just saw a talk on contact hole roughness. Interesting topic and one on which we haven't really focused. Key points were the 3 sig deviation of the contact hole from round and how these spokes as they were called contributed to electrical breakdown through the dielectric to the gate line due to the excessive electric field. The measurements shown were all SEM and therefor Top CD only. Might be interesting the characterize non-circular contact contours inside the contact at MCD and BCD.
One more paper on CER which i submitted in MNE conference. You can see the details in given link http://www.wangpengfei.freetcp.com/science?_ob=MImg&_imagekey=B6V0W-524WDXN-2-1&_cdi=5657&_user=4861547&_pii=S0167931711001110&_origin=browse&_zone=rslt_list_item&_coverDate=02%2F10%2F2011&_sk=999999999&wchp=dGLbVtz-zSkWA&_valck=1&md5=11f1f1f317a091fc007da320e9d8ad53&ie=/sdarticle.pdf