#!/usr/bin/perl
use strict;
use warnings;

PARSE:
while (<DATA>)
{
    chomp;

    next PARSE if /^\s*$/ ; # skip blank lines
    next PARSE if /^\s*#/ ; # skip comments

    # do something useful with the data
    print "<$_>\n";
}

__DATA__
some data here
# a comment
# another comment, followed by a blank line

more data
# another comment

final data