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You could always filter them out via Webmaster's tools.

Here's Google's official docs on it. http://support.google.com/webmasters/bin/answer.py?hl=en&answer=1235687

So, like million threads out there I lost my rank for a particular page and is looking to bounce back. However there might be something different in my case, hence the thread.

1. The rank drop was an after effect of design change, where we merged two pages together. Page A - which was ranking for Keyword A and Page B which was ranking for Keyword B. So we merged it together in the sense that both had similar content and design except the meta tags and page title (I wasn't involved in this project so...) and Page B gets kicked out of Google web index. Page A still remains number 1 for Keyword A.

2. There was some shady link building contract that was implemented some 3 months back (again me not involved, I joined later) and there were an unnatural number of links created with a striking artificial anchor text pattern from low quality "built for link building" blogs. I presume this also affected page B. as this effort was done only for Page B and not A.

So now, I managed to clear all the pages for duplicate content, implement a better page structure where I deleted out possible similar pages, redirected them (301) to main pages, and created a new page for Page B, like Page B1 with different content. Implemented a better internal linking profile too where terms related to Page B (Keyword B, Keyword B1, B2 etc) links to Page B.

Its been two months now, and Page B ranks for Keyword B1 but not the original Keyword B. I suppose the "penalty" still remains in Google.

Any clues how I can get around this?

What I want to achieve is to get ranked for Keyword B for Page B, if not the first result, at least start all over from a lower rank but at least break out of the penalty.