Theres an easy way and a hard way.
Edit the template to remove the part that shows the links, you would probably be looking for the template tag wp_list_pages http://codex.wordpress.org/Template_Tags/wp_list_pages which would probably be towards the bottom of header.php or at the top of index.php. If its the index.php it would probably also be in other files like page.php etc.
If its a theme you downloaded I'd maybe suggest posting the name/download link for it, maybe someone would be familiar with the theme or be able to download it to take a look and give a more definite answer.
Alternatively install http://wordpress.org/extend/plugins/exclude-pages/
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