due to the nature of my site, i see i have keywords high on the list in webmaster tools that i dont want, but unfortanutley are used a lot within the content of my site.

Is there a way to specify ignore certain words to a search engine or would i have to redesign site to not use those words, would be difficult?

You may write a fresh content for your website and avoid the unwanted keywords in that. Or just check out your meta keywords and description to see if that unwanted keywords are present there. Remove from there. Do SEO on all the important keywords with proper landing pages, you will see the desired results in short span of time.

Avoid using repetition of unwanted keywords in meta tags, description tags that has no value. Instead add value contents to your webpages with using such keywords.