open my $fh, '<+:raw', $file; # raw so file is read/written in bytes, not characters
my $where = tell($fh);
while (<$fh>) {
    ...; # modify 1 or more bytes
    seek $fh, $where, SEEK_SET;
    print $fh, $_;
    $where = tell($fh);
}
close $fh;