Well, there are issues with your second script that others have pointed out, but why not just put the first one (which you say works) inside a loop that loops through each file?

#!/usr/bin/env perl
use strict;
use warnings;
use autodie;

@allfiles = <C:/Users/user/Desktop/DOwork/filez/nabillingscript/09_14_
+2012/nas/*>;
 
foreach $file (@allfiles) {
    open (FILE ,"<", "Myfile");

    ###-reads each line from the file and splits it by multiple spaces
    while($lines=<FILE>) { 
        @kbused = split(/\s+/,$lines); 
        push(@kilo, $kbused[2]); 
    }   
     
    ####-takes the number from column2 and removes the KB from the end
    foreach $aline (@kilo) {
        $aline =~ s/\D//g; 
        push (@onlynums, $aline);  
    }

    $sumof += $_ for @onlynums;
    print "$sumof\n";
    close FILE;
}
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