This may get you started. Note that it does not find the top 100 words, it counts all words over 4 characters long.

use strict;
use warnings;
use Text::ExtractWords qw(words_count);

my %words;
my @paraStats;

local $/ = '-100';
while (<DATA>)
    {
    chomp;
    s/[\n\r]/ /g;
    my %paraWordFreq;
    words_count(\%paraWordFreq, $_, minwordlen => 4);
    push @paraStats, {%paraWordFreq};
    map {$words{$_} = 0} keys %paraWordFreq;
    }

my $col = 0;
print ' ' x 17;
for (sort keys %words)
    {
    next if 4 > length $_;
    $words{$_} = ($col += 1 + length $_);
    print "$_ ";
    }

my $paraNum = 1;
for (@paraStats)
    {
    printf "\nParagraph %5d: ", $paraNum++;
    my $col = 0;
    my %paraWords = %$_;
    
    for (sort keys %paraWords)
        {
        next if 4 > length $_;
        printf "%*d ", $words{$_} - $col - 1, $paraWords{$_};
        $col = $words{$_};
        }
    }
    
__DATA__
The first row is top 100 frequent words (in the text file). Numbers in
+ each cell
shows the frequency of the word in the data. The data is one text file
+ (.txt)
with more than 100000 words.
-100
Each "paragraph" is delimited by "-100". I need a matrix which shows t
+he
frequency of each word in each paragraph. I thought it is words-by-wor
+ds matrix,
but it's wrong. It's words-by-paragraph matrix. Thank you very much! P
+eace of
the world.
[download]

Prints (note that the lines are long:

                 100000 cell data delimited each file first frequency 
+frequent it's matrix more much need numbers paragraph peace shows tex
+t than thank thought very which with word words words-by-paragraph wo
+rds-by-words world wrong 
Paragraph     1:      1    1    2              1    2     1         1 
+       1                1                 1                     1    
+2    1                             1    1     2 
Paragraph     2:                          1    1                      
+                                                    1 
Paragraph     3:                               2                    1 
+            2      3         1    1                 1     1     1    
+           1       1    1     1         1                        1   
+           1     1     1
[download]