Well it may not qualify as removing them, but one way to acheive this is to put a cq:allowedTemplates property on the top node of you site heirarchy. So for example if you site is located below /content/mysite and all of your templates were located in /apps/mysite/template/ you could add a property to /content/mysite/jcr:content named cq:allowedTemplates and set it equal to /apps/mysite/templates/*. That would prevent any templates other than your custom templates from showing up. See http://dev.day.com/docs/en/cq/current/developing/templates.html#Template Availability for a more detailed review of all the factors that can influence template availabitlity. You can see the impact of this setting at play by looking at the differences when creating a new page in the various Geomettrix demo sites (most of which have the cq:allowedTemplates set at the top level).
A less prefereable solution would be to deny read access to templates in question - but that could cause other potential problems.