Hopefully this isn't offensive, but personally I'd rewrite your code as:

print "Enter file name and path of .ins to parse:\n";
my $filename1 = <STDIN>;
die "File $filename1 does not exist\n" unless (-e $filename1);

print "Enter file name and path of .rcs to search:\n";<br>
my $filename2 = <STDIN>;
die "File $filename2 does not exist\n" unless (-e $filename2);

open (FILE, "<$filename1) or die "Can't open file $filename1 :$!\n";
my @file = <FILE>;
close FILE;

foreach my $line (@file) {
[download]

Depending on what you're parsing here, I'd probably use a split rather than $1. YMMV.
ie: If file line was "EditorName Susan Hammel" I'd do

if ($line =~ /EditorName/) {
my @name = split(/\s+/, $line); 
my $first = $name[1]; 
my $last = $name[2];
}

foreach my $line2 (@file) { 
if ($line2 =~ /EditorCommand/) {
  my @commands = split(/s+/, $line2);
  shift @commands; # To remove the EditorCommand - Requires line that 
+looks like "EditorCommand print paste copy"
}

open (OUTPUT, ">>test.txt");

foreach my $com (@dcommands) {
  my $pattern = $word1 . ":" . $com;
  my $test = in_file($pattern, $filename2);
  if ($test) {
     print OUTPUT "Found $pattern in $filename2 \n";
  } else {
     print "$pattern not in $filename2 \n";
  }
}

exit;

#### SUBS ####

sub in_file {
  my $pattern = shift;
  my $filename2 = shift;

  open INFILE, $filename2 or die "Can't open $filename2: $!\n";
  my $found = 0;
  while (<INFILE>) {
     if (/$pattern/) {
        $found = 1;
         last;
     }
close FILE;
return $found;
}
[download]

HTH, YMMV
'Fect