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

PARSE:
while ( my $line = <DATA> )
{
    chomp $line;
    next PARSE if $line =~ m{ ^ \s* $ }xsm;

    next PARSE if $line =~ m{ ^ \s* # }xsm;

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

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

more data
# another comment

final data