my %ignore;

# First pass
while (<FH>) {
   $ignore{$1} = 1 if some_condition($_);
}

# Second pass
# reset the file to the beginning
seek FH, 0, 0;
while (<FH>) {
   if (m/matches interesting string with (capture)/) {
       if (exists($ignore{$1}) {
           next; # don't print this line
   print;
}