You can access more advanced features provided by CSE for added control and customization:

Refinements and Labels
Refinements are labels that you apply to web sites. They appear as a list of links above search results, offering users a way to narrow their search. When a user clicks a refinement label, the sites that you have labeled are given priority in the results. In addition to labeling sites, you can also specify words that are added to users’ queries when they click a label, providing even more targeted results.

Excluding sites
While AdSense allows you to filter ads by URLs, you can also filter URLs from your search results within your CSE account.

Collaboration
Collaboration is an optional feature for Custom Search Engines which allows other trusted users to contribute to your Custom Search Engine. Contributors can add sites to include or exclude in your search engine and apply search refinements to them.