You can pretty-print your document, apply XSL transformations, evaluate XPath expressions and change the document encoding. The results of XSL transformations and XPath evaluations are presented in a new document.
Changing the encoding is not just a matter of converting the characters that make up the document: the parser ensures that the output document is well-formed XML (e.g. by applying character entities and adjusting the charset pseudo-attribute of XHTML meta elements).
All processing tools require well-formed input.