How to strip whitespace-only text nodes from a DOM before serialization?

You can find empty text nodes using XPath, then remove them programmatically like so:

XPathFactory xpathFactory = XPathFactory.newInstance();
// XPath to find empty text nodes.
XPathExpression xpathExp = xpathFactory.newXPath().compile(
        "//text()[normalize-space(.) = '']");  
NodeList emptyTextNodes = (NodeList) 
        xpathExp.evaluate(doc, XPathConstants.NODESET);

// Remove each empty text node from document.
for (int i = 0; i < emptyTextNodes.getLength(); i++) {
    Node emptyTextNode = emptyTextNodes.item(i);
    emptyTextNode.getParentNode().removeChild(emptyTextNode);
}

This approach might be useful if you want more control over node removal than is easily achieved with an XSL template.

Try using the following XSL and the strip-space element to serialize your DOM:

<xsl:stylesheet version="1.0"
 xmlns:xsl="http://www.w3.org/1999/XSL/Transform">

  <xsl:output method="xml" omit-xml-declaration="yes"/>

  <xsl:strip-space elements="*"/>

  <xsl:template match="@*|node()">
    <xsl:copy>
     <xsl:apply-templates select="@*|node()"/>
    </xsl:copy>
  </xsl:template>

</xsl:stylesheet>

http://helpdesk.objects.com.au/java/how-do-i-remove-whitespace-from-an-xml-document