Here is how I solved my problem.

1. I get the directory present at specified depth.
2. Create new directory with altered name
3. Used FileUtils (Apache Commons IO) to copy the files to the new folder.
4. Manually delete all those old folder.

package com.so.practice;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import org.apache.commons.io.FileUtils;

public class Sof {
    public static void main(String[] args) throws IOException {
        List<File> files = getDirs(new File("path to root folder"), 0); //level 0 is inside parent , level 1, and so on
        System.out.println(files);
        String[] paths = new String[files.size()];

        int i = 0;
        for (File file : files) {
            paths[i++] = file.getAbsolutePath();
        }
        String matchword = "Folder1";

        //File  f = null;
        HashMap<String, String > old_new = new HashMap<>();
        for (int j = 0; j < paths.length; j++) {
            System.out.println(paths[j]);
            String old_path = paths[j];
            String foldername = new File(paths[j]).getName();
            //02_PA__OPCON.MES.GC.Configuration 
            //02_Configuration

            if(old_path.contains(matchword)){
                paths[j] =paths[j].replaceAll(matchword, "Directory");

                old_new.put(old_path, paths[j]);

            }else{
                System.out.println("skipping->"+old_path);
            }
            //f = new File(paths[j]);
            //f.mkdirs();
        }

        for(String key : old_new.keySet()){
            FileUtils.copyDirectory(new File(key), new File(old_new.get(key)));
        }

        //FileUtils.copyDirectory(new File(old_new.get), new File(arg0));
     }

     static List<File> getDirs(File parent, int level){
        List<File> dirs = new ArrayList<File>(); //to store 
        for(File f: parent.listFiles()){
            if(f.isDirectory()) {
                if (level==0) dirs.add(f);
                else 
                    if (level > 0) dirs.addAll(getDirs(f,level-1)); //recursion
            }
        }
        return dirs;
    }
}

something like this should do (Windows version):

import java.io.*;

public class RenameFile {
    public static void main(String[] args) {
        // change file names in 'Directory':
        String absolutePath = "C:\\Dropbox\\java\\Directory";
        File dir = new File(absolutePath);
        File[] filesInDir = dir.listFiles();
        int i = 0;
        for(File file:filesInDir) {
            i++;
            String name = file.getName();
            String newName = "my_file_" + i + ".pdf";
            String newPath = absolutePath + "\\" + newName;
            file.renameTo(new File(newPath));
            System.out.println(name + " changed to " + newName);
        }
    } // close main()
} // close class

http://people.apache.org/~jochen/commons-io/site/apidocs/org/apache/commons/io/DirectoryWalker.html

Implement the rename into String normalizeName( String ) and use:

public class FileRenamer extends DirectoryWalker {

  public List rename(File startDirectory) {
      List results = new LinkedList();
      walk(startDirectory, results);
      return results;
  }

  protected boolean handleDirectory(File directory, int depth, Collection results) {
      return true;
  }

  protected void handleFile(File file, int depth, Collection results) {
    String newName = convert( file.getName() );
    File file2 = new File( file.getParentFile(), newName )
    file.renameTo( file2 )
    results.add(file);
  }
}

new FileRenamer.rename( baseDirectory );