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

Without looking at your code it would be impossible to tell what's wrong.

      2. How can I access sub tree of the main tree?

You should probably be asking this at mailinglist for the xml library you are using.
If you are using xerces you might want to have a look at jdom(http://jdom.org), the api is a lot simpler. 
Check out XPath support, XPath will make things a lot easier.

      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?  

As with 2 you could also have look at XSLT.

      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 ?

Have a look at asm(http://asm.objectweb.org
specifically this class org.objectweb.asm.xml.Processor
It lets you generate xml documents directly out of class files.