XML Exception while Parsing from String to DOM error

In my code, I am converting DOM object to String object and replace few strings and again writing to DOM object.

While doing so, am traversing many files, code works first time while for 2nd file, while writing to DOM object , java exception thrown.

I know root cause, as two root element for xml has getting generated , however don't have idea to eliminate

Java exception occurred: 
org.xml.sax.SAXParseException: The processing instruction target matching "[xX][mM][lL]" is not allowed.

    at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)

    at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)

@ Code
doc = docBuilder.parse(fXmlFile);
TramsformerObj.transform(DOMSource(doc),StreamResult(writerObj));

% Replace String
try
StrObj = writerObj.getBuffer.toString.replaceAll(Sourcestr,Replacestr);
catch ME
    disp(ME.message)
end

% Convert String to DOM object
try
    isObj.setCharacterStream(java.io.StringReader(StrObj));
    docm = docBuilder.parse(isObj);
catch ME
    disp(ME.message)
end

PS:- Note all object/ variables are available in memory and accesible. This code is of MATLAB, am invoking all packages of JAVA in MATLAB