import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.text.DecimalFormat;
import java.util.Stack;

public class ReverseRoot {

    public static void main(String[] args) throws IOException {

        BufferedReader br = new BufferedReader(new FileReader("Test.txt"));
        Stack<Double> stack = new Stack<Double>();
        String str;
        while((str = br.readLine()) != null)
        {
            String[] tokens = str.trim().replaceAll("\\s+", " ").split(" ");
            for(String st : tokens)
            {
                if(!st.equals(""))
                    stack.push(Double.parseDouble(st));
            }
        }

        br.close();

        final String decimalFormatStr = "0.0000";
        DecimalFormat df = new DecimalFormat(decimalFormatStr);
        while(stack.size() != 0)
        {
            System.out.println(df.format(Math.sqrt(stack.pop())));
        }

    }

}

> BufferedReader br = new BufferedReader(new FileReader("Test.txt"));

http://acm.timus.ru/help.aspx?topic=judge
The program must be a console application.
Input data must be read from the standard input (input from the keyboard). Output data must be printed to the standard output (screen output).

Thanks a lot for pointing the issue.
I will change the implementation and repost it.