> Now I'm trying to stores these files in an array and compare them.
> How can one store the entire file in an array?
XML is a tree structure and a single array isn't really designed to be the most intuitive or simple way to store a tree.

> Now I have to compare the two XML files
Comparing XML files is a problem many people need to solve these days so a CPAN search might help. After looking through the modules in the CPAN search results and some experimenting I came up with XML::SemanticDiff. The sample code and output might give further ideas on how the module might be applied to the posted problem.

use strict;
use warnings;

use XML::SemanticDiff;

my $x = XML::SemanticDiff->new;
my @diffs = $x->compare(
    <<EOXML_1,
<top>
    <firstTag>abc</firstTag>
    <secondTag>def</secondTag>
    <thirdTag>ghi</thirdTag>
</top>
EOXML_1
    <<EOXML_2
<top>
    <firstTag>abc</firstTag>
    <secondTag>456</secondTag>
    <lastTag>ghi</lastTag>
</top>
EOXML_2
);

foreach my $change (@diffs) {
      print "$change->{message}\n\tin XPath context $change->{context}
+\n";
}

__END__
Character differences in element 'secondTag'.
        in XPath context /top[1]/secondTag[1]
Child element 'thirdTag' missing from element '/top[1]'.
        in XPath context /top[1]
Rogue element 'lastTag' in element '/top[1]'.
        in XPath context /top[1]
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