Execute a CommandLine Program from Java

That's OK. You probably need to handle the process' streams though. Read this carefully

http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html

try:

           Process p = Runtime.getRuntime().exec(new String[] { "cmd", "/c", "start", "filecrypt", "--encrypt", "filenames[i]", "--user", "PublicKeyName"} );

though by the looks start is unecessary and can be removed.
I'd also include the full path to your executable

and make sure you include the required command line options so the app does not prompt you for any input (or you will need to provide it) and run silently without any output.
Keeps the code simpler and avoids need to add the code shown in these examples
http://exampledepot.com/egs/java.lang/WriteToCommand.html
http://exampledepot.com/egs/java.lang/ReadFromCommand.html

Objects, I tried doing this. I tried printing the array variable, seems like variable "command" isn't getting assigned with the string.
Thanks for the help

public class enCryptFiles
{
      public static void main(String args[]) throws Exception
      {
         String[] filenames;
          File f = new File(args[0]);
          filenames = f.list();
          for(int i=0; i< filenames.length; i++)
        {
           String[] command = new String[] { "cmd", "/c", "start", "filecrypt", "--encrypt"+ filenames[i] + "--user", "PublicKeyName"};
         System.out.println(command);
         System.out.println(filenames[i]);
         Process p = Runtime.getRuntime().exec(command);
        }
    }
}