コード完成。
 /*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */
package jfile;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.net.URL;
/**
 *
 * @author andy
 */
public class JFile {
    /**
     * @param args the command line arguments
     */
    static File master = null,
                m1     = null, // file output with "001"
                m2     = null; // file output with "002"
    static FileWriter fw1,
                      fw2;
    static FileReader fr = null;
    static BufferedReader br = null;
    public static void main(String[] args) throws FileNotFoundException, IOException
    {
         String root = System.getProperty("user.dir") + "/src/files/";
         master = new File ( root + "master.txt" );
         m1     = new File ( root + "m1.txt");
         m2     = new File ( root + "m2.txt");
         fw1     = new FileWriter(m1, true);
         fw2     = new FileWriter(m2, true);
         fr = new FileReader (master);
         br = new BufferedReader(fr);
         String line;
         while((line = br.readLine())!=null)
         {
             if(line.contains("001")) 
             {               
                 fw1.write(line + "\n");
             } else if (line.contains("002"))
             {
                 fw2.write(line + "\n");
             }
         }
         fw1.close();
         fw2.close();
         br.close();
    }
}
プロジェクト Netbeans : http://www.mediafire.com/?yjdtxj2gh785cyd