I think what you're looking for is the /m modifier. This allows ^ and $ to match newlines in multiline data. Since it appears you need to worry about multiline queries (otherwise, why are you modifying the record separator in the first place), I changed your data to include one.

$/ = ";\n";

while (my $line = <DATA> ){
   $line =~ s/^#[^\r\n]*//mg;
   print "Query: $line\n";
}

__DATA__
# one comment
# two comment
# another comment

insert into table_name 
values(1, 'testing 1 2 3');
# more comments
insert into table_name values (2, 'test &#149;');

[download]
...gives... 
Query: 



insert into table_name 
values(1, 'testing 1 2 3');

Query: 
insert into table_name values (2, 'test &#149;');

[download]

You could also add $line =~ s/^\s*$//mg; if you want to get rid of some of those blank lines.

-Bird
Update: I like insensate's solution for removing the blank lines better. Use that one. :)

In reply to Re: Record Separator affecting Regex by Bird
in thread Record Separator affecting Regex by Kozz

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