I hope the previous replies have solved the immediate problem for you, and you are getting stuff stored into your target file. Just a couple more comments about the code you posted:

• If a line from the input file does not contain any of the patterns that you are altering via "s///", that line will not be printed to the output file. Is this what you want?
  
• You are doing a lot of redundant typing. One of the nice things about Perl is that you can write scripts with an absolute minimum of repetitive lines of code.

If you actually want the output file to have the same number of lines as the input file (with some lines being edited), it's pretty short and simple:

use strict;
use warnings;

my $inp = "source.cbl";
my $out = "source.ada";

open INP, '<', $inp or die "Can't open $inp: $!";
open OUT, '>', $out or die "Can't open $out: $!";

while (<INP>) {
    s/WORKING -STORAGE SECTION\./declare/;
    s/PROGRAM -BEGIN\./begin/;
    s/DISPLAY/PUT/;
    s/ACCEPT/GET/;
    s/PROGRAM -DONE\./END;/;
    print OUT;
}

close INP;  # no worries for closing input file
close OUT or die "Can't close $out: $!";
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