If you [right-click] [vertices] and then mouse drag and select all vertices then hit delete it should only get rid of the vertices that have 2 or less edges applying to them.

As always I would save your work before hitting delete but I have never had any problems with it.

You should watch out for vertices you have left with just two edges attached to them (happens sometimes when you have half a model ready for -x duplication) as they will be deleted too.