It seems to work for me, unless I misunderstood your specs. Here are the files I am using:
patterns.txt 
A[0]
C
D

[download]
infile.txt 
A[0]
B
C
D[0]
D1
DA

[download]
brut.pl 
#!/usr/local/bin/perl
use strict;
use warnings;

if (@ARGV != 3) {
    print "Usage: $0 <pattern file> <input file> <output file>\n";
    exit;
}

my ($pattern_filename, $source_filename, $dest_filename) = @ARGV;

open my $pattern_fh, '<', $pattern_filename or die "Failed to open $pa
+ttern_filename: $!";
my @tokens = ();
while (my $line = <$pattern_fh>) {
    chomp $line;
    push @tokens, quotemeta($line);
}
my $pattern = '^(?:' . join('|', @tokens) . ')[^a-zA-Z]*$';
print "Search pattern: $pattern\n";

open my $infile, "<",  $source_filename or die "Failed to open $source
+_filename: $!";
open my $outfile,">>", $dest_filename   or die "Failed to open $dest_f
+ilename: $!";

while(my $line = <$infile>) {
    print "input : $line";
    if ($line =~ /$pattern/) {
        next;
    }
    print "output: $line";
    print $outfile $line;
}
close($infile);
close($outfile);

[download]
perl brut.pl patterns.txt infile.txt outfile.txt 
Search pattern: ^(?:A\[0\]|C|D)[^a-zA-Z]*$
input : A[0]
input : B
output: B
input : C
input : D[0]
input : D1
input : DA
output: DA

[download]

In reply to Re^5: Search and delete lines based on string matching by imp
in thread Search and delete lines based on string matching by Anonymous Monk

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