There are two sets of tags you can use to limit the Kontera analysis on your pages:

Zone Tags tell our JavaScript where to analyze. They are useful in keeping our links out of nav bars, headers, footers and titles. You can use them multiple times on any given page, just please make sure you open and close each tag separately.
 
Filter Tags are used in order to define an area of the page where ContentLinks™ should not appear. All other areas of the page are valid mark areas. Please use these tags with caution in order to prevent a situation where large areas are filtered unintentionally.
 
Preventing words in your header, footer, and sidebar from being highlighted ultimately improves your overall CTR and eCPM.