Hi,
your are using $line too much.
For each individual scope you should add  my $line;.

#!/usr/local/bin/perl -w
use strict;
use warnings;

open (INFILE, "<$ARGV[0]") or die "unable to open file";
open (OUTFILE, ">$ARGV[1]") or die "unable to open file";

while (<INFILE>)    {
  my $line = $_;
  print OUTFILE replace($line);
}

sub replace {
  my $line = shift;
  chomp ($line);
  $line =~ s/data//;
  $line =~ s/=//;
  $line =~ s/detector//;
  return $line."\n"; 
}

close(INFILE);
close(OUTFILE);
[download]

Sorry, pasted the wrong statement.
Now it is correct.