Maybe something like...

my $line;
while ($line = <CONF>) {
    my $string;

    # check for start of virtual host block    

    if ( $line =~ /^\s*\<VirtualHost/ ) {
        $string = $line;  #no chomp

        # read in the enter virtualhost block...

        do {
            $line = <CONF>;
            $string = $string . $line;
        } until $line =~ /^s*\<\/VirtualHost\>/;

        # Find the server name

        $string =~ /ServerName\s+(.*)\s/;

        # Ignore it if necessary...you can add a number of checks here
        # including multple servers that you want to ignore.

        if ( $1 ne "my.domain.here" ) {
            print <CONF.NEW> $string;
        }
    } else {
        # if not a virtual server line, just pass it through.
        print <CONF.NEW> $line;
    }
}
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---

Dr. Michael K. Neylon - mneylon-pm@masemware.com || "You've left the lens cap of your mind on again, Pinky" - The Brain