I'd try to use glob in scalar context:

while (my $matchingFiles = glob("*.rtsd001")) {
   ...
}
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Though that doesn't seem to your real problem - in your current version you already have only one filename in memory each time.

I'd rather think your problem is @fileContents, which can hold the contents of an entire file. Instead of reading a file, selecting lines, storing those, and printing the result, you can just print them line by line:

               while (<UNMODIFIED>) {
                    /STRUC20/ and print MODIFIED $_;
               }
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