my @newlines = grep{/\S/}@lines;  #move only lines that have 
                                  #a non whitespace char to the left
or
@lines = grep{/\S/}@lines;

##</code><code>##

while (<FH>) # update: was: while (my $line = <FH>)
             # don't really need "my line" here
{
    next unless /\S/;  #skip blank lines
    next if /^\s*#/;   #skip comments, or whatever...
    blah, blah
}