I noticed you used the s modifier in your match and that you seem to be trying to match across the whole file.

This example might not be the most efficient way but is a start.

use warnings;
use strict;

my @terms = qw( Maple Oak walnut pine juniper );

my $text;
{
    #slurp the whole file
    local $/;
    $text = <DATA>;
}
if ( $text =~ /upperboundary(.+)lowerboundary/s ) {
    $text = $1;
    print $text, "\n\n";
}
else {
    die "no match";
}
foreach my $term (@terms) {
    if ( $text =~ /($term)/is ) {
        print "$1\n";
    }
}

__DATA__
upperboundary
The book Hiking the Red, A Complete Trail Guide To Kentucky's Red Rive
+r Gorge 
made it a point to describe the habitat and the diverse species of tre
+es that 
one is likely to encounter at the Red. According to the authors, the s
+pecies 
of trees found in the Daniel Boone National Forest includes beech, sug
+ar 
maples, white pines, hemlock, several types of oak, and hickory. These
+ trees 
provide habitat for an estimated 67 different species of reptiles and 
amphibians, 46 species of mammals, and 100 species of birds. 
lowerboundary
[download]

Edit: The text is from http://www.redrivergorge.com/dbnf.html.