BufferedReader in = new BufferedReader(new FileReader("file.in"));
BufferedWriter out = new BufferedWriter(new FileWriter("file.out"));

String line = in.readLine(); // <-- read whole line
StringTokenizer tk = new StringTokenizer(line);
int a = Integer.parseInt(tk.nextToken()); // <-- read single word on line and parse to int

out.write(""+a);
out.flush();

If the directory doesn't exist you need to create it. Java won't create it by itself since the File class is just a link to an entity that can also not exist at all.

As you stated the error is that the file cannot be created. If you read the documentation of PrintWriter constructor you can see

FileNotFoundException - If the given string does not denote an existing, writable regular file and a new regular file of that name cannot be created, or if some other error occurs while opening or creating the file

You should try creating a path for the folder it contains before:

File file = new File("C:/Users/Me/Desktop/directory/file.txt");
file.getParentFile().mkdirs();

PrintWriter printWriter = new PrintWriter(file);

There is semicolon right after you while loop

while(scan.hasNextLine());
//                       ^

which makes it infinite loop because it represents empty instruction, just like

while(scan.hasNextLine()){}

so you are never actually entering

{
    String stringRead = scan.nextLine();
    pw.println(lineNumber + ": " + stringRead);
    lineNumber++;
}

block, and code after it which means you are not writing anything to your result file and you don't even close it. All you have if empty file created with

FileOutputStream fos = new FileOutputStream("C:\\Users\\Reid\\Desktop\\rulicny.txt");

So remove this semicolon.

BTW you can easily spot this kind of mistakes if you will let your IDE format code for you. Eclipse formatted your example for me as

while (scan.hasNextLine())
    ;
{
    String stringRead = scan.nextLine();
    pw.println(lineNumber + ": " + stringRead);
    lineNumber++;
}

which as you see shows it quite good that your loop actually executes empty statement instead of code block.