Untested: 
use autodie;
my %file1;
my $max = 0;
my $min = 0xFFFFFFFF;  # Or 0xFFFFFFFFFFFFFFFFF with 64 bit ints
open my $fh1, $file1;
while (<$fh1>) {
    chomp;
    $min = length if $min > length;
    $max = length if $max < length;
    $file{$file1} = 1;
}
open my $fh2, $file2;
LINE: while (<$fh2>) {
    for (my $l = $min; $l <= $max; $l++) {
        next LINE if $file{substr $_, 0, $l};
    }
    print;
}

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In reply to Re: compare two files | Help by JavaFan
in thread compare two files | Help by fnicholas

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