String s = "», ∆, û, Ê, Ë, ö, , ä, é";
    	System.out.print("==> "+s);
    	s = s.replace('»', 'C');
    	s = s.replace('∆', 'C');
    	s = s.replace('û', 'z');
    	s = s.replace('Ê', 'c');
    	s = s.replace('Ë', 'c');
    	s = s.replace('ö', 's');
    	s = s.replace('', 'd');
    	s = s.replace('ä', 'S');
    	s = s.replace('é', 'Z');
    	
    	System.out.print("\n--> "+s);

==> », ∆, û, Ê, Ë, ö, , ä, é
--> C, C, z, c, c, s, d, S, Z

import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.UnsupportedEncodingException;


public class replaceAndCreateOutput {
    public static void main(String [] args) {
        String fileName = "primjer.srt"; // The name of the file to open.
//        System.out.println(Charset.availableCharsets().keySet().toString());
        
      try {
        FileInputStream fis = new FileInputStream(fileName);
        BufferedInputStream reader = new BufferedInputStream(fis, 64);

        FileOutputStream fos = new FileOutputStream("out_"+fileName);
        BufferedOutputStream writer = new BufferedOutputStream(fos, 64);
        
        byte[] buffer=new byte[64];
        int byteRead;
        
        while ((byteRead=reader.read(buffer,0,64)) >=0 ) {
          String inputString = new String(buffer, 0, byteRead, "windows-1250");
          
//          String inputString = new String(buffer, 0, byteRead, "MacRoman"); 
//          inputString = inputString.replace('»', 'C');
//          inputString = inputString.replace('∆', 'C');
//          inputString = inputString.replace('û', 'z');
//          inputString = inputString.replace('Ê', 'c');
//          inputString = inputString.replace('Ë', 'c');
//          inputString = inputString.replace('ö', 's');
//          inputString = inputString.replace('', 'd');
//          inputString = inputString.replace('ä', 'S');
//          inputString = inputString.replace('é', 'Z');

          System.out.print(inputString);
          writer.write(inputString.getBytes("UTF-8")); //destination file encoding. Za primjer sam uzeo UTF-8. Treba staviti onaj koji ti treba
        }
        
        writer.close();
        fos.close();
        reader.close();
        fis.close();
      }
      catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
      }
      catch (UnsupportedEncodingException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
      }
      catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
      }        
        
    }
}