Without looking at your code it would be impossible to tell what's wrong.
I m facing the following problems: -
1 After every import of the file that my Jython cmd.exe dint response and so every time I have to open the new cmd.exe to import my jython file
You should probably be asking this at mailinglist for the xml library you are using.
2. How can I access sub tree of the main tree?
As with 2 you could also have look at XSLT.
3. How can I retrieve the value of all the attributes of the elements of xml file after parsing so that I can use those values of the attribute in other file?
Have a look at asm(http://asm.objectweb.org)
4. Is there any way to parse my java file and present it in the form of xml file format or simply after parsing represent it into xml file ?