Try something like this; it out performs most other methods I've seen. You might want to try adjusting BUFSIZE. 64k works best on my system, but your's may differ.

Updated: Corrected handling of partial buffer.

#! perl -slw
use strict;
use constant BUFSIZE => 65536;

chomp( my $searchTerm = $ARGV[ 0 ] // 'five' );

open BIGFILE, '+<', 'theFile' or die $!;

my $readPos = my $writePos = 0;
my $buffer = '';
while( <BIGFILE> ) {
    $readPos = tell BIGFILE;
    if( ! m[^\Q$searchTerm\E] ) {
        $buffer .= $_;
        if( length( $buffer ) > BUFSIZE ) {
            sysseek BIGFILE, $writePos, 0;
            syswrite BIGFILE, $buffer;
            $writePos = sysseek BIGFILE, 0, 1;
            $buffer = '';
            seek BIGFILE, $readPos, 0;
        }
    }
}

if( length( $buffer ) ){
    sysseek BIGFILE, $writePos, 0;
    syswrite BIGFILE, $buffer;
    $writePos = sysseek BIGFILE, 0, 1;
}

truncate BIGFILE, $writePos;

close BIGFILE;
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