print "What is the name of the access rights .csv? (Full file name)\n"
+;
my $file = <>;
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That would be better written as:

print "What is the name of the access rights .csv? (Full file name)\n"
+;
chomp( my $file = <STDIN> );
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print "Is there a header in this file?\n";
my $header = <>;
if ($header =~ m/^yes|^y]/i){
    $header = "1";
}
else {$header = "undef";
}
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At this point $header will ALWAYS be true.    I think you meant $header = undef; instead of $header = "undef";.

open (CSV, "<", $file);
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You should always verify that the file opened correctly before trying to use an invalid filehandle.

open CSV, '<', $file or die "Cannot open '$file' because: $!";
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