Yes, if you go into administration console you can set a variety of Field or Template-specific permissions. Repository > Metadata Management > Templates, then select a template and click the Security button in the lower-left corner of the window. 

Completely removing a user/group's access to a template will hide it from the drop-down.

However, you'll probably need to do some testing and planning because they probably have access through the Everyone group, and you'll need to have group-based permissions in place before removing that to make sure no one loses access.

The way we do this is by having our users in role-based groups, then we grant each group access to templates as needed. We have an administrator group that gets full access to every template, and we remove the "Everyone" group's access.

I would highly recommend testing this outside of your production environment first because there are a lot of permissions and you want to make sure you get it all sorted out before making sweeping changes.