This code could stand a lot of improving. I suggest you start from scratch and do things the "right" way (to name a few: don't open, read, reopen, then reread files just to get the Nth line, don't assign to $., don't pass data to subs using global variables, don't clobber $_, etc)... Tie::File will save you a lot of time. I suggest something like this:

use strict;
use Tie::File;

foreach my $file (readdir DH) {

    ## skip hidden files
    next if $file =~ /^\./;

    my @lines;
    tie @lines, 'Tie::File', $file
        or die "Couldn't open $file: $!";
    
    ## skip files where the first line contains "Clock"
    next unless $lines[0] =~ /^Clock/;
    
    ## grab CSV timestamp info from 4th line and last line
    my $start = ( parse_csv( $lines[3]  ) )[0];
    my $end   = ( parse_csv( $lines[-1] ) )[0];
    
    ## prepend lines to the file: modifying the array modifies the fil
+e
    unshift @lines, "PREPEND LINE1",
                    "blank,blank,blank,$start,$end";
}
[download]

You should also consider using Text::CSV or Text::CSV_XS for parsing CSV data, so you don't have to worry about maintaining that CSV regex.

blokhead