Please see perlfaq5:

       How can I use Perl's "-i" option from within a program?

       "-i" sets the value of Perl's $^I variable, which in turn affec
+ts the behavior of "<>"; see perlrun for more details.  By modifying 
+the appropriate variables
       directly, you can get the same behavior within a larger program
+.  For example:

            # ...
            {
               local($^I, @ARGV) = ('.orig', glob("*.c"));
               while (<>) {
                  if ($. == 1) {
                      print "This line should appear at the top of eac
+h file\n";
                  }
                  s/\b(p)earl\b/${1}erl/i;        # Correct typos, pre
+serving case
                  print;
                  close ARGV if eof;              # Reset $.
               }
            }
            # $^I and @ARGV return to their old values here

       This block modifies all the ".c" files in the current directory
+, leaving a backup of the original data from each file in a new ".c.o
+rig" file.
[download]

That is one approach, using <> by setting @ARGV. If you simply wish to work on another filehandle, look at the first question in perlfaq5 ("How do I flush/unbuffer an output filehandle? Why must I do this?"), where it states how to set per-filehandle variables (like $| and our desired variable $^I):

# Long, understandable version
$old_fh = select(OUTPUT_HANDLE);
$^I = '.orig';
select($old_fh);

# Short version
$^I = '.orig', select $_ for select OUTPUT_HANDLE;
[download]

or if you wish to keep the new OUTPUT_HANDLE selected, simply select( OUTPUT_HANDLE ); $^I = '.orig'; Good luck!

Update: Trying to actually answer the question.