please note that the transformation of xml related objects is a circle of 3 services:
Dependend on which type you start with and which one you need for further processing you have to use one or two of them using the output of the first one as input on the second one.
The service pub.xml:queryXMLNode should exactly do what meets yor requirement.
See IntegrationServer Build-In-Services Guide for further informations on these services.
Can you share your IS version as well as some error messages from the server log (if there are any)?
Can you share a sample of your document structure as well as the query you have already tried for queryXMLNode?