We have a website www.example.com and the same has also been set as preferred domain from Google Webmaster Tools. But the problem is for some reasons there are more than 50 duplicate sub-domains (not sure if this the right terminology) indexed and listed in Google, Yahoo, Bing. All of them shows the same content as the original domain because in UltraDNS *.example.com points to www.example.com
For example wwwww.example.com, www31.example.com, www.wwww46.example.com, etc. are all crawled and displayed in the SERPs (may be in the 3rd page or may be in the 9th page). Even a few have the same Page Rank as the main website!
I guess this is a case of url canonicalization and are negatively affecting the rankings of the main domain as i) They are considered as duplicate contents ii) PR/weightage getting shared
I think the best way to handle them is to do a 301 redirection for all of them for the next 60-90 days, let the SEs update their indexes and them just terminate them.