Now how do I read each filename in perl?

Well, that depends on how your program is supposed to get the filenames. Is it all files from a certain directory? Use opendir and readdir. Are the filenames given through a pipe? Use <>. Are the filenames the command line arguments? Then they are found in @ARGV. Do you use command line options to communicate filenames? Use Getopt::Long (or some other Getopt:: module).

The way I have written the code, DSSPIN produces the error:

My advice is to stop using bareword file handles. That's so last millennium. Use autovivifying filehandles:

my $filename = "....";
open my $fh, "<", $filename or die;
while (<$fh>) {
    ...
}
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Autovivifying filehandles have been there since March 2000 - when 5.6.0 got released.