There are two major ways to ask the question "Does this string start with S?" in Perl. One method is to use a regular expression. The other is to use substr.

#!/usr/bin/perl 
use strict;      # glad to see you using strict.  Good job!
use warnings;    # lexical warnings are better the the -w switch, 
                 # becuase you can turn them off where appropriate.
                 # Good job using warnings, too.
use diagnostics; # diagnostics give verbose explanations of error mess
+ages.
                 # It can be very handy when you are just starting out
+.


# You had: open FNAMES,"</var/tmp/flist";
# I made several changes here:
# *  I switched to the 3 argument open.  It's avoids some potential 
#    security issues, and is generally considered to be the best 
#    way to go. 
# *  I am also using a lexical filehandle instead of a global handle.
#    This is generally considered to be the best way to go as well, 
#    for the same reasons that we prefer lexical variables with 
#    limited scope to global variables.
# *  Finally, I am checking the results of the open() call.  If the 
#    call fails I end the program and display an error message.  

open( my $filenames, '<', '/var/tmp/flist' )
    or die "Unable to open file list - $!\n";

while ( defined( my $fname = <$filenames> ) ) {
    chomp ($fname); # Added a semicolon


    # Regex based approaches:
    
    # Does the string start with an "s"?
    if ( $fname =~ /^s/ ) {
        $fname =~ s/^s/_S/; # Do the substitution

        # Do special stuff 
    }


    # Did we replace a starting 's' with '_S'?
    if ( $fname =~ s/^s/_S/ ) {
        # Do special stuff if we did a substitution.
    }

    # Using substr()
    #
    # Does the string start with an "s"?
    if ( 's' == substr($fname, 0, 1) ) {
        substr($fname, 0, 1) = '_S'; # Do the substitution
        # or
        substr($fname, 0, 1, '_S');  # Do the substitution

        # Do special stuff 
    }

    # Does the string start with an "s"?
    if ( 's' == substr($fname, 0, 1) ) {
        substr($fname, 0, 1) = '_S'; # Do the substitution
        # or
        substr($fname, 0, 1, '_S');  # Do the substitution

        # Do special stuff 
    }
}
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For this situation, I'd just do the substitution with a regex in the condtional test: if ($fname =~ s/^s/_S/) .... In fact, in most cases a regex is the way to go for looking into strings and finding stuff inside them. But sometimes substr is the way to go.

You've made a good start. Keep working, and you will see good results.