Oh man, Scrapebox is not a tool to use if you don't know what you to do with it.
You probably did one of the following:
(1) added too many links
(2) added too many links too fast
(3) didn't spin your anchor text
(4) didn't spin your comment
(5) left your comments only on heavily spammed pages
(6) tried to spam Matt Cutt's blog....
The solution to the above mentioned problems can be fixed as follows
(1) if you added way too many links, it might be better to just buy a new domain and start from fresh, you could always do a 301 redirect to your site. If you only added a "manageable" amount of links, try to use Google's disavow tool
http://support.google.com/webmasters/bin/answer.py?hl=en&answer=2648487
(2) Use the disavow link from some heavily spammed sites and slowly add new links
(3) Slowly add new links with VARIED anchor text
(4) Slowly add new links with different comments
(5) Disavow links
(6) Send Matt your full address, Social Security number, Blockbuster's member number because he's gonna come to arrest you
