You need to be sure to split each line from the input file into words before you check for stopwords. Here's a simplistic example. 
...
use Lingua::StopWords qw|getStopWords|;

my $stopwords = getStopWords( 'en' );

open my $infile, '<', 'fulltext.txt' or die "$!\n";
open my $outfile, '>', 'nostopwords.txt' or die "$!\n";

while (my $line = <$infile>) {
    my @words_all = split /\s+/, $line;
    my @words_nostop = grep { !$stopwords->{$_} } @words_all;
    print {$outfile} join( ' ', @words_nostop ), "\n";
}

close $infile;
close $outfile;

[download]

In reply to Re: How do I read in a document, remove the stop words and then write the result to a new file? by grg
in thread How do I read in a document, remove the stop words and then write the result to a new file? by demisheep

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.