I have an XML document having structure similar to the following
blaa
blaa blaa
You should be able to add an XPath-Transform to the Signature. It should look something like this:
...
I am not fluent in XPath, but it should be easy to formulate an XPath-expression that excludes the Footer-element. (But note that XPath is an optional part of XML-DSIG, so not all implementations may support it).
Alternatively, if you could restructure your document to be
blaa
blaa blaa
or
blaa
blaa blaa
you could handle it by using an Enveloped Signature Transform (first case) or by signing the signedEnvelope element (second case).